Standard for a caster PrC.
I suppose Knowledge (Arcana) is to make the class accessible to sorcerers, which is fine given they don't have Knowledge (Religion) as a class skill. However, I see two issues with the special requirement. First, you still cannot get into the class with Corpsecrafter since the requirements include Bolster Resistance, which has Corpsecrafter as a prerequisite. Thus, I suggest dropping the Bolster Resistance requirement altogether. Second, the Enhanced Undead class feature (and alternate class feature for necromancers) also gives the same benefits as Corpsecrafter, so I suggest adding it in as well.
I think you just copied the cleric's list of class skills and made a couple minor changes. Overall, I'd say Diplomacy makes absolutely no sense for a master of undead. Profession could be useful if the charater is expected to pass as a non-necromancer with a full-time job, but then you should add Bluff to the list of class skills as well (and possibly Disguise). You also forgot to add the tags to each skill, like (Con), (Int), (Wis), or (Cha).
Seems standard.
The last line is very powerful and should be its own separate abilities (I suggest you take a look at the Yathrinshee and the Green Star Adept to see how official classes dealt with such ability). Though I don't think that keying it by character level is really a good idea. The Abjurant Champion gets a similar class feature, but it is its 5th-level capstone. Like with the Yathrinshee, only levels in a caster class (or with abilities like Practiced Spellcaster) should count.
Character level again? This should really be caster level.
Why not let the Lord of the Undead choose a bonus feat of his choice from a small list? Does Deadly Chill make more thematic sense than Hardened Flesh or Nimble Bones for some reason?
Hey, I have a suggestion here. Why not let them pick a domain of their choice from a small list? Also, any reason arcane spellcasters get more benefits from the domain than a cleric does (such as more domain spells per day and the ability to cast domain spell spontaneously)? I suggest you make the ability work as Arcane Disciple for arcane spellcasters (without the need to pick a deity or to apply it to a single arcane spellcasting class, obviously).
No, you worked backwards here. As written, if a spell isn't on your list, you cast it at +2 caster level. If it is, then it gets added to your list a second time (which is fairly useless). I also see no reason to separate arcane from divine casters here. Simply add these spells on the character's class list(s) and list of spells known, state that they get a +2 bonus to caster level with these spells if they already know any of them or are a prepared caster who gets these spells on his class list, and call it a day.
You are making a contradiction, first stating it applies to all attack rolls, then only to those made with natural weapons. Also, there is no such thing as damage reduction /unholy. There is damage reduction /evil, but not /unholy.
What if I stack Enhanced Undead, Undead Mastery, Corpsecrafter, Desecrate and this ability all together? How many bonus hit points would my undead get?
LotU? Also, why do Personal spells suddenly end up with a better range than Close spells, Touch spells, and in some case Medium range spells?
Does it stack with Hardened Skin?
Actually more of a fluff ability.
Undead already use Charisma for everything that normally involves Charisma, so you should rewrite it as just adding a bonus to their Fortitude saves equal to their Charisma modifier. Maybe also add a minimum of +0, so undead with really low Charisma don't get penalized for it. Also, +10 Charisma over 10 class levels? You should rather put a lower limit on Charisma based on level, so that zombies can actually end up with a Charisma of 11 (at 10th level in the class) without giving a +10 bonus to Charisma to things that are already high on it, such as any incorporeal undead (who as written effectively get +5 AC).
Summon? So even if the undead is killed it will reform at its normal location in 24 hours? I think this brings the term expendable minion to a whole new level. You can basically afford to lose 1 minion/2 class levels a day and have them back by tomorrow.
This... doesn't work like that. A dread necromancer 20 gets 320 HD of undead (assuming a Charisma of 34). A cleric 5/wizard 5/mystic theurge 10 gets 120 HD. A character with this feat gets caped at 64 HD (assuming a 34 in the relevant ability score). As written, the class feature nerfs the character instead of helping him. I still don't see any way dread necromancer is going to help; for that it should be "adds his Charisma modifier * class level to the amount of undead he can control with Animate Dead", or similar. Also, removing the HD cap on Animate Dead is just plainly broken. Even with the nerfed control limit, you can control a 64 HD skeleton, which by the rules has a CR of 19. While a minion with a CR of 19 is not the worse you could do at 20th level, it is still better than a cohort, and you get to add all kinds of nifty things to it, including 512 bonus hit points (from Corpsecrafter + desecrate + the dread necromancer class feature or the wizard alternate class feature + improved corpsecrafter). Definitely broken, especially with optimization.
This needs some reworking.
So this ability is for Create Undead. Fine. Now you won't be getting a 64 HD skeleton. You will be getting a 64 HD bone creature.
Fine, so your 64 HD bone creature is surrounded with an infinite amount of 12 HD or less skeletons. At least you have a good lieutenant to control them when you're away.
Swarm Shifter is a template applied to an undead creature. It does not turn a living creature into an undead, unlike the others on the list. Also, I think a monster's CR should remain a meta concept, not something that dictates how the rules work. Most of the time, a monster's HD and CR are close to each other. But in the cases where it isn't (I dunno... bone creature evolved spirit naga?), you can get some pretty good stuff (a huge-sized, 27-HD creature with 7 levels of sorcerer casting, a BAB of 20, and a poison with a save DC of 31 for 1d8 Con damage, all for CR 17). At the other extreme, you can control an infinite amount of 1st-level paragon corpse creatures (elite zombies?) or 12th-level swarm shifter death knights, thanks to an earlier class feature.
These are kind of big benefits, aren't they? However, their purpose (a 9th- and 10th-level capstone) is obvious.