(Disclaimer: never touched 3.0 before now)
I really, really like the Master of Flies from Savage Species. But a few things seemed off about its description, such as the flying beetle swarm (which I couldn't find anywhere as a monster). I dug around a little and found out that the class is actually a 3.0 class, and some more digging in 3.0 monsters and spells revealed that swarms were not creatures but spell effects! This made the Master of Flies a bit more confusing, if playable. Still, I'd like to try and adapt some of his class abilities to be more 3.5 friendly. Namely Swarm Shape, but a few others as well (I'm pretty sure that using his swarm charming ability as it is right now results in the MoF getting eaten alive by the swarm).

I'm not touching the prerequisites yet, even though they're technically outdated right now. I want to focus on the class abilities. Let's start with the biggie.

Spoiler: The reasoning for changes
Swarm Shape: Swarms didn't exist in 3.0, so the rules given here no longer mesh. For starters, the swarm starts as a medium creature and eventually becomes a Huge creature. According to the swarm subtype, though, swarms can only ever take up 4 squares and are still the size of their component creatures. (There's also a bit about dispersion, which was a way of dispelling swarm spells, but that doesn't exist anymore so we're just going to ignore that. Wind effects are included by virtue of the swarm's size category)

There's also some weirdness in that the swarm is based off of an outdated Summon Swarm, including a type of swarm that doesn't exist anymore.

There are two fixes I can see for both of these. Let's start with the size and space issue. In option one you simply break the rules- make the MoF's swarm take up only one square at lower levels, normal swarm size at level 5, and a Huge creature's space at level 8, splayed out however the MoF wants so long as every square is connected. It's simple, but also a bit demure. It doesn't seem like that would feel like a swarm at all, and nobody's going to enter the class so they can charm vermin- no, they want to be a huge swarm, crawling all over the bad guys and messing with clumps of enemies.
If you want to follow the rules a bit more strictly (and make the MoF much scarier) you could do what the swarm subtype says to do to represent bigger swarms of bugs: more swarms. This option would see the MoF change into a full-size swarm at 2nd level, and gaining the option to 'add' extra swarms later on. These could have the restriction of needing to remain connected to each other, or perhaps just within 30 feet (so allies still have room to fight bad guys, too). Their hit points are shared regardless of distance- damage one, you damage both. For the purposes of area attacks, the two swarms are one (if a fireball catches both in the blast, the MoF rolls only one reflex save and takes damage only once, though he still takes that nasty 50% extra from being a swarm).

Next up is the issue of the swarms themselves. First up, the standard swarm traits would apply. The save DC for distraction would be based on his MoF levels, as would his swarm damage (or would that be better based on HD like a normal swarm?). After that, there are two roads to take as to what the MoF actually gets from his swarm shape:

It could be something similar to the original, in that the MoF takes on a standard swarm template with only minor changes depending on the bugs involved. As the original, movement would be 15 ft across all swarms, 45 (clumsy) if they fly, and most ground-bound bugs would have a standardized poison. And maybe a climb speed. There'd probably be more base insects at 1st level, rather than unlocking locusts later on.
It could also be much more of a wild shape ability, letting the MoF take the shape of any vermin (and only vermin) with the swarm subtype. Just like wild shape, he gets their special (ex) attacks, but not special qualities with the exception of swarm traits (he is treated as having a hive mind). This allows for much more variety and very interesting swarms, but only if you've got access to more than the monster manual. The HD limit would be MoF level +5, since it takes at least 5 levels in another class to get in.

Summon Swarm doesn't need much of a change, but it could use another flying swarm, since the beetles don't exist. It could specify a beetle swarm that uses the same stats as a bat swarm, minus blindsense and wounding abilities and fine rather than tiny (and thus immune to weapons). Also, since the summon swarm spell is no longer random, neither should the ability be.

Pied Piper is fun, but potentially lethal. It just needs to specify that the vermin stops before entering the MoF's square, so the poor bugger doesn't get ripped apart when using it on swarms. You could specify that it's a mind-affecting charm effect that works on mindless vermin, but that's linguistic nitpicking at this point.

Finally might want to add an ability that makes the MoF immune to her own swarms and resistant to others. What's the point of being a terrifying bug-monster if you can't stoically stride through a squirming mass of voracious insects?

Oh, and considering that 3.5 lets fireballs nuke swarms so effectively, maybe it wouldn't hurt to give the poor bug a good Reflex save.

Additional: The 'calm yo swarm' and Bug Shape abilities are last minute additions thought up while writing this. The first allows the MoF to be more of a team player- the shape lasts for hours, after all -without giving them the ability to cherry pick targets for what is, effectively, an AoE attack. You would figure an intelligent swarm would be able to stop ripping things apart, if not exactly to top ripping things here and keep ripping them there, but I can't find rules for it so I included a line about turning swarming off. The Fly on the Wall just seemed like a logical conclusion to a bug-themed character, more a tool for villains that could also be well exploited by PCs. But, it being last minute, I haven't really thought ahead to any far-reaching consequences.

Spoiler: The Changes
Summon Swarm (Sp): A Master of Flies can use Summon Swarm once per day per level in this class at a caster level equal to her character level. The creatures summoned must be vermin, but she can summon a swarm of beetles that function as a bat swarm without the wounding or blindsense abilities, and are fine instead of tiny.

Lord of the Flies (Ex): The Master of Flies takes no damage from swarms she has summoned and is not subject to their Distraction ability. She subtracts her class level from damage dealt to her by other swarms, and adds the same number as an insight bonus to all saves against their abilities.

Swarm Shape (Su): Beginning at 2nd level, the Master of Flies can take the form of a vicious vermin swarm. This ability functions similar to Wild Shape used by a druid of 5 levels higher than the Master of Flies' class level, except as noted here. The Master of Flies can only take the form of of a diminutive or fine vermin with the swarm subtype. She gains all swarm traits, including immunity to critical hits and flanking, immunity to weapon damage (though not special abilities like Frost or Flaming), immunity to trip, bull rush, and grapple, and immunity to any spell or ability that targets a specific number of creatures (such as Disintegrate). She takes half again as much damage (+50%) damage from effects that affect an area, cannot make grapple, trip, or bull rush attempts, and is subject to wind effects as a a diminutive or fine creature. She has a hive mind, and thus gains no immunity to mind-affecting effects. Her swarm damage is 2d6 +1d6 for every 5 levels in this class, dealt to any creature whose space she occupies at the end of her move. The save DC for her Distraction ability is 10 + Her Master of Flies level + her constitution.

As a free action, the Master of Flies may calm her swarm to allow allies to share her space. In this state she deals no swarm damage, and her Distraction ability is nonfunctional. This affects the whole swarm- she cannot specifically target squares that contain her allies.

At 2nd level, her swarm is 4 contiguous squares. They must be connected, but otherwise the shape is up to the Master of Flies. She decides her arrangement at the end of each movement. At 5th level, the swarm grows larger, and the Master of Flies becomes two swarms. They must remain connected, but otherwise their shape is still decided by the Master of Flies. The swarms cannot overlap to deal more swarm damage. They share a single hit point total and act simultaneously. If both swarms are caught in an effect that affects an area, they are treated as a single entity- the Master of Flies rolls a single reflex save, and only takes damage once (though she still takes +50% damage for being a swarm). At eighth level, the Master of Flies can instead become three swarms, following the same rules as above.

A master of flies returning to her normal form (voluntarily or otherwise) may appear in any unoccupied space in the swarm's area.

Pied Piper (Su): At 3rd level, a Master of Flies is able to influence vermin to a limited extent. She can use this ability once per day per level in this class to charm a number of HD of vermin up to her character level, starting with the lowest HD vermin in range and up to the highest until the HD limit is reached. When the Master of Flies uses this ability, affected vermin within 10 ft per level in this class must succeed on a Will save (DC equal to 10 + Master of Flies level + Cha) or become captivated. This is a sonic mind-affecting charm effect, but can also charm mindless vermin, even swarms. A creature that successfully saves cannot be affected again by the same Master of Flies' song for 24 hours.

A captivated victim walks toward the Master of Flies, taking the most direct route available. If the path leads into a dangerous area (through flame, off a cliff, or the like), that creature gets a second saving throw. Captivated vermin can take no actions other than to defend themselves. (Thus, a centipede cannot run away or attack but takes no defensive penalties.) A victim within 5 feet of the Master of Flies stands there for as long as the Master of Flies concentrates, offering no retaliation to any attack. When the Master of Flies stops concentrating, that vermin is immune to her Pied Piper ability for 24 hours.

Fly on the Wall (Su): At 4th level, a Master of Flies can use one of her daily uses of Swarm Shape to become an undetectable bug. She can take the form of an individual member of any swarm she could become with Swarm Shape. Her movement speeds are equal to that of the swarm, but she cannot make any attacks while in this form. She gains a bonus on Move Silently checks equal to half of her size bonus to hide (+6 for a diminutive creature, +8 for a fine creature).

It's been some time since I tweaked classes and whatnot, so any feedback at all would be very helpful. I don't want to go too far overboard with this adaptation, just modernize it. And maybe go a little overboard.

Speaking of overboard, have some feats. I know that prestige classes don't really get their own feats, but I was having fun. These will be more silly than the class tweaks above.

Spoiler: For swarming PCs

Animal Swarm
Pre: Know (Nature) 12 ranks, Class Feature that specifically targets vermin
Ben: When using any class feature that specifies vermin, you may instead specify animals. If using Swarm Shape to take animal form, the maximum size is Tiny instead of Diminutive.

Swarm Split
Pre: Single hive mind with two or more swarms that cannot seperate
Ben: You may split your swarms into multiple, independent creatures. You decide how many swarms separate (up to your component swarms) and assign them any number of hit points (up to half your maximum), which you lose when the swarm splits. You divide yourself on your initiative as a swift action and your multiple selves can move any distance from you so long as you maintain line of sight. You are still a single hive mind (the swarms are not separate consciousnesses). If the swarm moves out of your line of sight it begins to take intelligence damage at a rate of 1/round. A swarm that reaches 0 intelligence this way is severed from you and becomes mindless until you can re-establish contact (by moving into its space). Rejoining with a split swarm is a move action that heals whatever hit points were lost at the split. If the original swarm has since healed, any extra hit points are gained as temporary hit points that fade after one hour.

Pre: Swarm Subtype
Ben: You no longer deal swarm damage to allies, nor are they subject to your Distraction ability. Your allies never need to make concentration checks because of your swarm.
Normal: Your allies are only protected from your swarm damage if you stop dealing swarm damage (including to enemies)

Plague Wall
Pre: Swarm Subtype, Fly Speed, Bastion
Ben: As a move action, you may whip your component creatures into a harmless frenzy that hampers vision. You are treated as a wall that provides concealment through one square of your swarm, or total concealment through two. Movement ends this effect.

Plague Armour
Pre: Bastion, Swarm Subtype, Size Diminutive or Fine
Ben: This feat allows you to wrap yourself around an ally like a wriggling mass of armour. As a full-round action you can surround any ally whose space you share, giving them a +2 bonus to their natural armour and DR 1/-. Whenever the damage they take is reduced because of this DR, you take 1 point of damage that bypasses your weapon immunity. Every medium creature benefiting from your protection removes one square from the area of your swarm, every large ally removes 4 (meaning that a typical swarm can only cover a single large creature). You can cover multiple creatures, but doing so requires a concentration check as a standard action (DC 5 +5/creature beyond the first) every round and any ally that moves out of your area loses the benefits of this feat (and returns one square of swarm to you). If you calm your swarm (dealing no swarm damage or Distraction to anything) this DC lowers by 5. Failure on this check ends the effect for all allies.
If an area effect includes creatures armoured by you without including spaces occupied by your free-flying swarm, you do not take extra damage from it. (A fireball would only deal +50% damage if it hit both a square where you were using this feat on an ally and one where you weren't. If you use this on a single large creature, losing all of your swarming squares in the process, you can't take extra damage from such a fireball)

Mass Awaken
Pre: Awaken Vermin, Pied Piper
Ben: When using Pied Piper to charm a mass of vermin, you may use a single use of your Awaken ability to affect each vermin that you have charmed. You can also now use your Awaken ability on swarms, granting them a hive mind.