A core character-building system that has levels but is, in and of itself, classless.
At least 10 example classes created, from 1st to 20th level, using that system.
A mechanic to encourage roleplaying. World of Darkness has vices and virtues, where you gain basically 'action points' by acting in accordance with either one. It also has a morality system where you can acquire various penalties to your character as you commit ever greater acts of evil (stealing stuff, hurting people, killing people, etc.). Perhaps not quite what D&D needs, but something ought to encourage people to roleplay a bit. I probably wouldn't need it in my game, but it'd be nice to have.
An optional combat system that does not require minis or maps.
A magic system that, like the character-building system, is fairly classless and non-setting specific.
At least 3 examples of taking the magic system and using it to create different styles of magic.
No more rolling for hit points.
Consolidated skill lists, akin to things you see in lots of recent d20 products. Sneak, Perceive, Influence, etc. instead of Hide/Move Silently, Search/Spot, Bluff/Diplomacy/Intimidate, etc.
Skills that are useful even at high levels. E.g., why do you need jump or climb when the wizard can cast mass fly? Why bother with hide and move silently when you can be invisible and silenced? This most likely will require altering spells slightly.
Clear rules for the "you're 20th level, so it's not a problem that he's got a crossbow pointed to your head" or "you're 20th level, so it's safe to jump off this cliff" issue. Just have them there to silence the naysayers and stop the frikkin' "D&D sucks because it's unrealistic" arguments. It's time they came up with some new reasons to think D&D sucks.
So basically I want a D&D rules system that is designed to be a "Fantasy Adventure Game," so it can cover any sort of fantasy gaming you want. And then, because this /is/ D&D, a large chunk of the book would be devoted to presenting the standard tropes of D&D.
Sample classes would be cleric, fighter, thief, wizard; barbarian, bard, druid, paladin, and ranger. The DMG would have a chapter devoted to briefly discussing non-standard campaigns, and would have classes like assassin, monk, noble, psion, samurai, and sorcerer.
Likewise, the core magic system would be flexible, and the PHB would present plug-and-play components to turn the flexible system into bardic magic, cleric magic, wizard magic, and druid magic. Then the DMG would provide some other components for turning it into psionics, defiling, shadow magic, etc.