Changes
Dare I say consider abandoning d20 for the three d-6 system? I don't know the math involved, but I know some people get highly.... exercised... about the importance of the random die roll until your character's modifiers get obscene. They seem to think that 3d6 solves that problem. Sure, it won't happen and no, I don't especially favor this one way or another, but it's something I typically see.
Other concepts: Your Mileage May Vary
Have Sorcerers work off a separate spell list from wizards? Or introduce some artistic randomness to their repertoire? Have their familiars be different? Make them distinguishable from walking artillery by something other than their fashion sense?
FLAVA: Put description blocks for every spell you print. Use the manifestation description to expand that approach for them, so that spells have a smell, a psychic memory, and such.
Bards should have songbooks, like musicians do, and function like wizards off their spell list and not like now as kissing cousins to sorcerers. This would make them slightly less ... well, you know. Alternatively, just admit that the Beguiler's a decent way to build a bard and ditch the bard song?
If it's remotely possible, stop DnD from morphing into a super-power game after the characters reach 12th level or so? I've found that spells trump everything after a certain level.
More personalized summoning? Animals, fey and plants for druids, chaos creatures for sorcerers, the pretty monsters for the bards, etc.? ooh! Or how about this concept: a selection for the basic nine alignments, so that conjurers aren't bouncing all over the alignment spectrum?
A reputation system to replace the alignment system?