Design Manifesto, by SRD chapter, as envisioned by Eldan:
The basics: Keep them as close as possible to 3.5. The basics work.
Races: I think races are too similar. They should provide more features, more features that are relevant over a longer timespan, more interesting, and more balanced.
Base Classes: Every class should have: unique features that others can not easily reproduce. Interesting features. A choice between different, but thematically related features. The closest I can think of in core is the Ranger. Out of core, ACFs. These should be incorporated from the start. Classes should be as balanced as possible while maintaining their mechanical diversity. Balance isn't the strength of third edition, and not what I actually want from it. I want diversity and creative unbalance.
Prestige classes: Go back to these being optional, specialized builds. Give base classes enough features to make them attractive on all levels. Make prestige classes give up something for what they gain (i.e. no full casting prestige classes. Look at the DMG: the archmage gives up spells per day.)
Skills: Mostly leave them as they are, but incorporate skill tricks and other new abilities right into them. One big thing that annoys me is knowledge skills, though: they shouldn't depend on monster HD, but every monster should have an "exoticness" value.
Feats: Feats should never just add numbers. They should add abilities. The difference between feats and class abilities is that feats are beneficial to several different builds, while class abilities are specialized.
Magic Items: I'm not sure what to do with these, and I'll leave that to someone else. I would prefer less pure +number items.
Combat: combat maneuvers could probably stand to be a bit simpler, but if we are honest, most are attack roll, then opposed ability check, which is to be expected. Anything else? Mobility should perhaps be easier and more emphasized.
Magic: A few things. First, I dislike outright immunities, especially gained by spells. Second, no spells that are better than entire classes or replicate class features (invisibility, super-buffs, knock, find traps, etc. Especially a problem for skill monkeys). Third, what I did: make all spells that have large effects or permanently change something into rituals which are performed out of combat and take time and resources. 4E was on to something here, even if they did it wrong. Fifth, make spells easier to interrupt and resist at higher levels.
Monsters: Not sure what needs to be done here, not my thing. Not that much, really?
Types and Subtypes: Do any of these have to change? I remember someone showing how (Undead) could be a subtype, with humanoid (undead) vampires and construct (undead) skeletons, though that's going into details. Maybe have some of the types lose the straight immunities as well. Stabbing a construct in the weakpoint is perhaps harder, but not impossible.
Monsters as races: Ah, the big one. So many people want it. So many people have tried it. I've never seen anything quite satisfying.
Environments, et al: A few small things that are silly oversights like drowning, but overall okay, I think?