While we're busy getting rid of everything that d&d has ever done (vancian magic, pregenerated spells, classes and alignments).... why don't we consider getting rid of the name? I mean, that's really a sacred cow, right? D&D is really about generic fantasy gaming anyway, so why limit it by giving it such a specific name?
Since it's a new edition, we need to change some of the rules, but not change so many that the game is unrecognizable.
despite the fatbeard outcry over second edition settings, things like Planscape, Spelljammer, and Dark Sun are D&D. Fuck, I despise Eberron, but it's still D&D. Discussing creating a new system that is D&D needs to take something very specific into account - all of those settings, all the stupid shit that has gone into D&D for the last 30 years - all of it has to be able to find a place in that new system. yes, ropers and piercers and hook horrors are essentially lame, the flail-snail is one of the most silly-assed things i've ever seen, and dragons fucking everything that moves is kind of lame - but it's all a part of the long-term D&D mythos. books like
Lords of Madness and
Stormwrack still feature Spelljammer references, and Planescape is built right in to the cosmology now. Half-Giants and Thri-Kreen are built into the psionics handbook, a bit of a nod towards dark sun.
things that are actual design features of D&D, IMO:
Alignment - the law/chaos and good/evil battle is really one of the essential components - you may not like it in play, but it's one of the most basic parts of D&D. subjective morality is great in a lot of games - but D&D is a game of heroes, and clearly defined morality. get rid of clearly defined alignment, and you start getting rid of the gods of D&D.
Spells - Silly ass spells that have odd effects, that don't always match up to any given system. same goes for funky monsters that don't make any sense. I won't say that "prepared" spells are really the right way to go - the spontaneous casting setup is really another part of the vancian system, and I'd personally like to see some medium between preperation and spontaneous. I agree with gunhilda that there needs to be a stronger border between arcane and divine spellcasting. 3rd was nice in that it's all a single consistent system, but the constant overlap of spells has left the whole system bland and generic.
Classes and Multiclassing - always has been a bit wierd, and I think that the third edition design of multiclassing still needs a lot of work. 2nd & 1st edition multiclassing relied on being demihuman, while 3rd has the rather cumbersome favored class rules based on race. Theres a lot of wiggle room to be had in the way that races and classes interact, and I think that it's a place to take a good solid look at how you want to be able to customize characters. I think both fewer and greater limitations on multiclassing would be a good idea. One bit I actually liked in second edition was the breakdown of classes into catagories. the Warrior catagory had the fighter, paladin, and ranger. Magic-Users has wizards and the specialists. Rogues had Thiefs and Bards. Priests were Clerics and Druids. 3rd has tried to retroactively add those catagories again with the complete book, but that hasn't quite worked in the same flavorful way.
Skills & Feats - again, there's a lot of wiggle room here - between second edition nwp/wp proficiencies, and the 3rd edition skill/feat system, there's been a lot of changes, not all of it for the better. I think that a median position here would be a good idea again - a net decrease in complexity is important. Instead of balance, jump, tumble, etc... It might be worth while to roll it all into one skill. I think that IH's skill groups were a step in the right direction, but it's still a lot more paperwork than there really needs to be.
Races - heres where we get some really Iconic D&D stuff going on - Dwarfs are Fighters, Elves are Wizards with swords, Humans can do anything, Half elvs are there, and Gnomes and Halflings are short and no one cares about them anyway. 3rd edition humans are just too good, mechanically - Almost everyone i've played with since 3rd came out has played human. I think that the races need to be looked at rather seriously.
Psionics - psionics have always been the bastard stepchild of D&D, and I think that it really needs to be addressed. I'm not sure how to address it, but it bears consideration.