I have not read the whole thread yet, but I figured I'd build my own list and amend it upon further reading/thought;
1; Equality of classes. I also noticed people seemed against homogenization of classes, though I can't claim I think the classes were homogenized out of unique flavor. I can understand how it appears that way upon a cursory overview, as illustrated by one of my friends claim that a wizard was as good at fighting as a fighter if they both had an equal strength. However, each class does have unique mechanics which differ them from one another, the only homogenization happening in power and feat acquisition on the XP chart. But I won't begin to argue, as that's not the point of the thread, and I'm sure this horse has been dead a while, somewhere around here.
2; Magical items should be useful, but should not be necessary to keep up with the game's math. For example, if magical swords gave no bonus at all, but instead simply provided a cool effect, or provided a bonus only under certain circumstances (+2 to trip attempts, +1 to attack and damage undead, etc).
3; Since skill checks are essentially just modified stat checks, I would like to see the elimination of skills as they are, and instead make them straight stat checks, and each character can choose from a list of specialties which making any stat check to do that kind of thing provides a bonus.
4; No daily limits on anything. Get rid of the Vancian abilities altogether. Except for expendable items, the characters should be able to use all of their abilities in every combat. There's no reason to limit a character's ability to heal in-between combats. If they can heal three times every encounter (which is the same as five minutes, so three times every five minutes), then let them. There's no reason to limit that. "Sorry, you ran out of blood, my magic doesn't heal you any more" is an arbitrary limitation. The PCs will rest as long as they need to in order to recover either way, but my way doesn't force the PCs into a corner when they're almost done with the dungeon, but they ran out of their cool spells or ability to heal back up.