Me, personally?
Base Statistics
Hit points should be in the double-digits even at maximum level. I'd much rather have a nearly-fixed hit point system adjusted for size personally, but I find scaling hit points acceptable if pathetic as long as the ceiling is kept low. Defense and attack scores shouldn't go higher than 30-35 on a d20 scale. I'd love to implement a Shadowrun-ish dice pool system, but I'm afraid that D&D scales too much to keep the dice pools at an acceptable level. As far as attributes go, I say still keep them in the game but they should be kept at the mostly 'useless' level. I mean even more useless than in 2E D&D. They affect things like skills, attribute rolls, etc.. Combat and power statistics use a totally different metric, meaning that a level 9 Fighter little girl with an 8 in strength is still going to do just as well in battle as a level 9 Fighter bulked-out orc with a 20 in strength.
Levels
I prefer a three-tiered approach. With ACTUAL tiers, not the 4E bullshit stuff. Something like:
Levels: This works exactly like we've come to expect from D&D. I personally don't think that there should be more than twenty levels and I'm sympathetic to arguments that it should be shorter, like 10-15 levels. But you know how grognards get at bullshit minor changes, so keep it at twenty I suppose.
Epic Levels: At this point in the game, D&D resembles more of a wargame than squad-based combat. Everything gets renormalized again, though you're allowed to carry more things from 'regular' levels to 'epic' levels than sublevels to regular levels. You as the 1st-level Epic Paladin command entire paladin legions all riding silver and gold dragons. Epic levels end at level 10, when you're the overdeity who can make the Lady of Pain and Lord Yahweh suck your juicy balls. I'm not proposing anything specific, that would be an entirely new thread and in fact would be mostly incompatible with the rest of this list... just... you know, fan wanking.
Race should be a pretty big deal at lower levels, but as time goes on it matters less and less. By the 1/3rd mark of the game, most mundane races like trolls and drow shouldn't have much of a functional difference between humans and dwarves. Racial stuff is almost completely internal to the race itself; there won't be such a thing as racial class powers, feats, backgrounds, whatnot. I'm still on the fence about racial equipment. While I think it's acceptable for a level 1 orc fighter to generically bash heads better than a level 1 elf fighter, at level 5 (of 20) it's stupid.
Skills
As far as skills go, I favor a three-tiered system.
B) The second tier of skills will be the dicepool system. Skill ranks are intentionally kept pretty low. Mostly because the second tier is supposed to be intentionally limited and having numbers max out at 12-13 keeps people from trying to shoehorn in skills at high levels. But anyway they'll work pretty much like Shadowrun. Skills in the game have a soft cap to them; after a certain point in the game people just don't get skill-boosting stuff anymore. We'll also have to put in a note about skills just plain not being useful past a certain point and discouraging players from investing or relying on them.
C) The final part of the skill system, which comes after a certain level of play, is the skill talent system. All that bullshit about making a DC 120 check to balance on a cloud or doing algebra to determine how well someone can swim in full plate goes away. Fantastical stuff from now on is done by skill talents. As in rather than upping up your Climb skill, you take the Athletic Mastery skill talent which lets you run up vertical surfaces, do double jumps, swim for an unlimited amount of time, etc.. Athletic Mastery 2 lets you balance on water, do infinite double jumps, and walk on ceilings as easily as on the ground. People are still allowed to use their background and skill points to solve challenges, but challenges from here on out are generically built on the assumption of someone having Feat Talents. If people are that in love with rolling I suppose that you could have an internal rolling mechanic as well. Maybe having some skill DCs marked 'Epic' and only people with the appropriate Feat Talents being allowed to make skill check rolls on it (roll Athletics to see if you can cling to the side of a fissure while a 12.0 Earthquake rumbles and you're pelted with lava). I'd rather retire skills altogether personally.
I think the maximum amount of magical gear an individual player should have is 4 distinct items. But none of that '+1 Flaming Sword' shit; at the bare minimum magical items should be stuff like Holy Avengers. Magical gear should be completely random and the combat math should flat-out assume that parties don't have any magical items. Party items like flying carpets and immovable rods should be at around the level of 1 item per player. I'm okay with some magical gear being buyable or craftable (that way you could have Sentai-style parties where everyone had color-coded elemental armor), but the really good stuff should be random.
Action Points/Edge
Action points are dumb. They never have their intended effect of turning around a failing combat in a pinch and that's because it's generally more efficient to use them for a nova against a perceived difficult encounter. So fuck that. Characters should have Shadowrun-style Edge where you buy a reroll or extra points on the d20 roll after the fact.
Powers
D&D should, at least for the non-beginners, use Winds of Fate. No question. What should be the minimum and maximum size of the WoF matrix? I think it should start out at about 2x4 and they should be generically loaded so that people not interested in complexity would have access to a row of maneuvers that could cover a wide variety of situations (you could have them themed such as 'Medium Fire Blasting' or 'Unleash Rage which had things like Whirlwind Attack, Power Throw, etc.'), but also advanced players could pick-and-mix how they felt like. Forcing someone to always have a ranged attack is useful but it's also kind of dumb if the player doesn't actually want to have those attacks--though it should be emphasized that if a player fucks up at that point it's their own fault. The maximum size should be something like 6x6. I think that non-martial players should have a few 'extra' manuevers that they don't put into their WoF grid so that they can swap things around a bit if they don't like the feel of what they currently have.
Players should also have things like bullshit basic attacks, too--only we'll avoid the 4E pitfalls and go out of our way to make them the inferior option rather than allowing players to pump them up so that they're better than powers.
Multiclassing
I'm a huge fan of multiclassing. Unfortunately, I was very unsatisfied with the way 4E and 3E D&D did theirs. 4E's failings are obvious, so let's talk about 3E's for a brief bit.
All characters are divided into three classes: A Main Class, A Subclass, and a Minor Class. The Main class gives you about 50% of your powers and abilities, the Subclass gives you about 35%, and the Minor Class gives about 15% of them. In order to prevent bullshit like a Fighter 10 / Wizard 1 having access to just 1st level spells, the class features a Main Class/Subclass/Minor Class hands out are level appropriate. You can choose to make it so that each class division hands out unique powers or you can make it so that the class division tells you how many times you can dip into a list (such that a Main Class chooses three fighter abilities, while a Minor Class only gets to choose one) or you can do a combination. I recommend doing a combination to make classes feel more different but also to save on space. What you picked for your MSM classes also determines how many powers you can put from your class onto your WoF matrix. So for a 2x3 matrix, a Fighter/Wizard/Cleric can make, say, 3 powers come from Fighter, 2 come from wizard, and 1 come from cleric.
If you want to be single-classed, make all of your Main/Sub/Minor classes the same class.
Personally, I found 3E and 4E's front-loading of class features extremely unsastisfying. So I strongly believe that at certain level breakpoints people should get more class features.
Feats
I believe that we should use the Tome System of feats. Meaning that all feats start off generically equal in usefulness, they just 'power up' according to your level at certain breakpoints. Feats that do bullshit things like '+1 to your attack' should be fucking banned. But since feats will do a lot more and they will also level up, the amount of feats that people get should be smaller. I think handing out feats at levels 1, 2, 7, 12, and 17 (for a twenty-level system) should be sufficient.
Narrative Control Options (Fate cards, etc.)
Should totally go into the game. But, but but but I'd like to emphasize that Narrative Control Options should:
A) Combat NCOs should affect the overall tactical situation, not minutae. Meaning that you use them at the beginning of combat Stupid shit like 'your next attack knocks the enemy prone' should be banned, stuff like 'your enemies were infected by a virulent disease and take penalties for the duration of combat' or 'your enemies are facing an ammunition shortage and can only make one ranged weapon attack before running out of ammo' should happen.
B) Have a pile of non-combat NCOs and combat-affecting NOCs and you're not allowed to trade them.
C) Should be random and awarded at the beginning of the adventure. If the PCs can't figure out a way to use a NCO either because they lack imagination or it really is that useless for this situation, their loss.
D) Is a party resource, not a player one.
Disadvantages
A) Should be mandatory and have a minimum.
B) You don't get anything for picking one. You also don't get anything for picking extra ones.
C) Should have players pick at least one 'physical' disadvantage, one 'personality' disadvantage, one 'history' disadvantage, and one 'luck' disadvantage.
Contacts
A) Contacts should level up alongside the player. Either that means that they get more connected (the barmaid of the most famous inn gets picked up by the King and becomes his queen), they just get flat-out more powerful, or you trade in an old contact for a few one (thief guild chump Gary for the assassin guild leader).
B) Should top out at three per player; one is a 'combat' contact and can be convinced to come alongside a player for more perilous adventures (either investigating something simultaneously or if the DM feels like it even fighting alongside the player) and the other two are 'noncombat' contacts.
C) Should have clearly-defined 'abilities' a player can schtup them for if they don't feel like roleplaying the encounter out. For example, you can try to convince the Chancellor in a session to send you some aid and some guards to help you on your quest. Or you can just use the 'Information Schtup' ability and learn what he knows or the 'Bureaucracy Manipulation' ability and have him put the screws to the thieves' guild or audit Baron von Vampire.