dtgreene: It turns out that the actual Pun Pun setup can be done with the core rulebook using, of course, a full caster. Wizards can do it at level 17. Druids can as well; you just need some way to get a scaled companion (maybe summon a crocodile?). Clerics, who are generally considered overpowered as well, need the Animal domain to get Shapechange, but can still pull this off.
You
do need the Surrukh, though, and that does come from a rather obscure source. PunPun, at his core, is about combining the broken ability of the Surrukh with the broken game mechanic that is polymorph. Everything else in the formula is entirely incidental and meant to facilitate that gamebreaking interaction.
dtgreene: * The skill system is deeply flawed, especially considering how cheap it is to make items that provide ridiculous boosts to them. This, in turn, makes it nearly impossible to balance anything that uses the system for anything important, such as Epic Spellcasting (easily gamebreaking if you try to optimize it), or the Truenamer (worthless if you don't try to optimize it).
I'd disagree on that one. While there are problems with the way some skills (*cough*diplomacy*cough*) work by RAW, the scaling of the numbers is generally reasonable. Truenaming and Epic Spellcasting are just poorly designed subsystems, and the skill system was a poor fit for what they set out to do.
dtgreene: * Caster level is too important. This tends to make multi-class spellcasters pretty much non-viable, especially with the way multi-classing works. (They actually made some prestige classes to try and patch the issue; the Mystic Theurge being the most obvious example.) I don't like having the Magic Resistance mechanic, especially when saving throws already exist as a defense against spells.
If I multiclass Fighter/Barbarian, the base attack bonus is additive. If I multiclass Fighter/Wizard then the Wizard is still giving me half BAB progression. Caster level, on the other hand, gets
nothing from multiclassing. It really needed to get a similar treatment and have a stacking progression like everything else. That would also mean that non-casters would implicitly have a caster level, which could potentially have had interesting ramifications on the design of magic items.
My only issue with spell resistance is that evocation should have been SR: no. As a game mechanic, having some creatures that are extra resistant to magic is fine, especially given wizards have tools to get around it when it comes up. The bigger issue is that evocation as a school was just nerfed into the ground by all the unfavorable factors stacking against it, and it really didn't need SR as another one of those.
dtgreene: * All spells of the same level have the same save DC. This has the result that save-or-lose spells are far more powerful than things like save for half damage spells. It doesn't help that HP goes much higher in 3rd edition than in 2nd but spell damage doesn't, and that there is a widespread oddly-behaved ability called "evasion" that turns damage spells into save-or-damage but does not affect save-or-lose spells.
I'd say that's more an issue of the evocation school being underpowered. Save or suck spells are nasty, and many could have been designed better, but I don't feel the DC's themselves are the problem. Rather, the issue is with evocation as a school being underpowered. Even something as simple as making them SR: no would have done wonders for it.
Evasion is a potent ability, but it has limited distribution and isn't particularly common unless you're raiding a thief guild or something like that. Area of effect damage spells are just poor choices against those creatures, and I don't have a problem with some creatures just being highly resilient against certain categories of spells, particularly when the ability isn't all that common. Immunity to Mind-Affecting spells is the bigger issue, since it's absolutely
everywhere and it completely shuts down the entire Enchantment school, whereas Evocation still has some spells that don't hit reflex save.
dtgreene: * The healing situation has improved from 2nd edition, but there is still the issue that Heal is far stronger than lower level healing spells, and that healing during battle isn't usually a good strategy (before Heal, at any rate).
I don't really see an issue with any of that. 3E D&D is a fast-paced offensive game, and I don't see a problem with healing being a poor in-combat strategy. It's still very useful between battles, and the design of the Cleric class makes it easier to have healing powers without having to dedicate yourself to them. I don't see a particular problem with the Heal spell outclassing the Cure spell. Yes, it's a big shift in the power curve, but as far as broken spells go it's not even on the radar compared to the real offenders.
Otherwise I agree with your critiques.