It offers a save, works only at close range, SR, and is a [death] and [sonic] spell, so that's four or five points of failure.
Points of failure against what? Fireball offers a save, shocking grasp a touch attack, and scorching ray a ranged touch attack. Let's run some calcs on stuff you might encounter at the 17th or higher range.

First, our wizard's save DC. Assume base 18 Int, +2 from race, +4 from levels, +5 from wish, +6 from headband for a total of 35 (jumps to 36 at 20th level). Ad in an additional +2 from Spell Focus and Greater Spell Focus.

So that gives:

10 (base) + 12 (Int) + 2 (Feats) + 9 (Spell) = 33

Let's compare that to some of the opposition you might fight at level seventeen (Only stuff where fortitude is weaker than will):

-Aboleth Mage: Has a +15 save, saves on a eighteen or higher and has no defenses against Wail.
-Various Forms of Dragon (technically you're better off with Dominate Monster, but whatever): Save less than 50% of the time, no immunity.
-Marilith: Saves on a 14 or higher, or on a 19 or higher against Dominate Monster. No Immunities.
-Four Beholders: Not in the SRD, but they fail IIRC most of the time. Antimagic eye is a problem.
-Horde of Delvers (CR 9): Can't save. Die automatically.

So, yes it has several points of failure. But what was the last monster you fought that was actually immune to it?

(Seriously, who assumes no magical gear, when it's that easy and flexible and is required by the game?)
Sure. Give him his magic sword, magic armor, magic amulet, magic belt and magic cloak. What about that helps him escape?

The no magical gear point is twofold. The first is that it's not actually the fighter escaping if he uses his Anklets of Transportation - a commoner could do that just as well. The second is that magic items come from wizards.The fighter can't survive a wizard on his own, needing another wizard's help to not automatically die.

Four points of failure.
Stop saying that. It doesn't make the spell weak. Like, at all. The fighter also has way, way more points of failure.

Here's a list:
-Reach + AoOs
-On Another Plane
-Ethereal (technically a form of on another plane)

That's just off the top of my head. And many of those are "hard" points of failure. That is to say that a wizard can still beat a dude of he might save, because he also has a chance to not save. A fighter will not beat a dude on another plane. Those are also way, way more common. Dragons fly, have reach and brutal attacks, have good AC, have tons of hit points and can go invisible, ethereal or to other planes - that's every single thing on the list, and dragons are seriously almost half of high CR monsters.

They are bad design. However, they're not quite that bad. They're usually limited not just by saves, but by immunities, range, and spell slot.
That's not why they're bad design. They aren't bad design because they kill things too easily. They might be design you don't like, but they are in fact the best strategy for winning level appropriate encounters. They're bad design because it doesn't matter to the wizard what the fighter is doing and it doesn't matter to the fighter what the wizard is doing.

Look at it this way:

Fighter + Wizard
Round One: Fighter hits, monster takes damage. Wizard casts SoD, monster makes save.
Round Two: Fighter hits, monster takes damage. Wizard casts SoD, monster makes save.
Round Three: Fighter hits, monster takes damage. Wizard casts SoD, monster fails save. Monster dies.

Just Wizard
Round One: Wizard casts SoD, monster makes save.
Round Two: Wizard casts SoD, monster makes save.
Round Three: Wizard casts SoD, monster fails save. Monster dies.

The fighter did exactly nothing (well, maybe he tanked some hits) for the team in that fight. That's why a paradigm where some classes get SoDs and some just do damage sucks. If taking damage made saves harder, then the fighter would be synergistic at least.

This PrC fixes those three main problems by the fourth level, which pretty much makes blasting the most optimal strategy you can have, even at very low cheese levels (no metamagic reducers).
Show me the money. At what levels does this class do better against reasonable opposition than a "normal" wizard?

OK, how about Twin Split ray of frost out of a 6th-level slot that can do half again as much damage as disintegrate and with no save? (Average of 104 damage if all four attacks hit, which is fairly likely against most foes, since touch attacks are easier to land than spell saves, vs 77 if the target fails a save against disintegrate after the touch attack hits.)
That's not true. You have (assuming basic investment) a Dex bonus five less, no spell focus, and the level mod is largely the same.

But that's a sixth level slot that is stopped by Lesser Globe. And it isn't, say, circle of death which is a fort save to kill most level appropriate encounters.