1) Sorcerer- Seems fine, it will still be better/worse than the wizard in the things it's better/worse at.
2) Rogues - Seems fine, it's a question of precision, not necessarily vitals just as you say. Seems a little strange for elementals though, can you sneak attack a ball of energy with this idea? It's made of fire. It doesn't have joints.... Maybe you could give the rogue an option to trade SA dice that won't do anything for a bonus to hit the thing at all? A +1-10 bonus to hit against fortified targets could serve to offset things.
2.5) Criticals - Seems a bit potent for a Keen Falchion, which has an automatic 25% chance of hitting any monster in the game in the hands of a level 1 commoner, but honestly, your poor players are going to be the ones who suffer most, so if they're cool with this penalty against them, that's dandy.
3) Enchantments & Illusions - I see you don't like absolutes, but sometimes they make sense. Certain things are just plain immune to mind-affecting abilities. You can't make friends with a spider, it has no equivalent, it's programmed to bite and drink blood. You can't dominate the mind of an undead that has no mind because there's no mind to dominate, and you can't make an Elf sleep, because elves don't have the ability to sleep. If you take away sleep immunity, give those poor willowy buggers a bonus feat or something, make them catch up to humans a little. There's not really much else that gives enchantment/illusion immunity beyond True Sight (give it a caster level check as Dispel Magic for each illusory effect it encounters?) and Mind Blank (which admittedly only emulates mindlessness, doesn't cause it). I'm not quite sure, what's racially immune to illusions, other than Oozes?
4) Skills I was writing a lengthy question before I spotted your later explanation. All skills as class skills is far more reasonable, but in my own experience, part of the balance between classes is what skills that class can specialise in as much as the number of skills it has access to. A possibility I might recommend would be treating all skills except UM/PD and Knowledge as cross-class skills in terms of cap (1/2 level +1), but only costing 1 skill point to increase by 1 point. This may keep the intended class "bias" whilst encouraging characters to branch out into other things?
5) Classes - You've agreed with completing PrCs, which makes a lot more sense than the first idea stated.
6) Feats - More feats more fun. Sounds good to me.
7) Spells/Powers - No material component requirements or xp costs