It's kind of funny, but looking at this list, I'm not sure any of these are what I personally would want to make the "perfect" D&D, while a few are things I know I don't want at all.
Definite No, No, A Thousand Times Noes: Alignment, unless it's done like Level Up where it's a tag certain creatures have. Species as class, no, unless "human" was a species/class as well and/or there were as many classes for each species as there were for humans: elf fighter and elf thief and elf cleric. And there was a way to represent someone being raised by a different species or in a different culture. And no level limits. No encounter abilities either, because--to me, at least--that feels very combat-oriented. Like, can I cast fireball a hundred times if I'm not in combat, or can I only cast it if I'm in combat? Maybe I want to turn a desert into glass! At least with "once/rest," I feel like I can use it outside of combat, if necessary.
Kits/Prestige Classes: No, because they lead to both bloat and imbalance. I prefer the Synergy Feats from LU, which are practically prestige classes anyway.
Class Archetypes: Sure, unless there's a better way to show differences within wach class without it becoming too bloated.
Psionics as a separate system: Sure. Actually, what I'd prefer is if each of the spellcasting classes had a distinct method of spellcasting. Maybe wizards do slots, but clerics have prayers that are unlimited but get progressively harder to have answered until you can spend time engaging in the appropriate rituals/prayers/sacrifices/deeds that your religion requires; and sorcerers have to spend hit points or even Hit Dice; while warlocks would be more like clerics but would have to engage in the ritual/prayer/sacrifice/deed each time the spell is cast; and bardic spells are... I don't know yet.
Actually, I'd also be happier if there were fewer caster classes.
Complex Martials: Sure, martials need more love. Level Up's maneuvers are a good start, although they may be too complicated. Perhaps something like Battlemaster maneuvers, but more extensive and for all martials, not just one archetype.
Advantage/Disadvantage: It's simple, it's elegant, so why not. Include LU's expertise dice to allow for more gradations.
Save or Die/Suck: On the one hand, they're cool in concept; on the other, they're a pain. What I would prefer is for some effects to last longer. You're poisoned or drained or charmed for hours or days, not just a minute. But there should also be ways to reverse each possible effect, possibly even non-magically. If you can get the completely mundane antivenin, you're cured of the poisoned condition. If not, well, you might be poisoned and get sicker, and even die. Just not right away.
Level Drain: No. Not unless you can come up with a way that fixes the annoying math. Perhaps instead of losing a level, you permanently have to roll a dX and subtract that from your rolls and Hit Point max, with the size or number of dXs depending on how many "levels" you lost.
Rulership/Leadership/Warfare Rules: Sure, sounds good. Not necessarily my thing but I think it's good for the game as a whole.
Paths to Immortality: Here's a thought I had: You get up to X level--heck, just call it 36th level for right now--in more than one class (i.e., you have to multiclass to become Immortal). Once you do, you gain the ability to grant warlock spells. Your own warlock levels don't count in reaching 36th level. You also have to be dedicated to a god (or force, philosophy, whatever) of some sort, maybe even be at least a 1st-level cleric, because you're basically becoming a saint/exarch of that god.
20 Levels/Epic Rules: Well, they keep saying most people don't reach 20th level, so maybe it doesn't need it. On the other hand, some people really like playing Epically, so maybe make the higher levels the Epic ones and make the lowest levels far weaker in comparison.
Species Choice: Include lots of species, but make sure to say that it's up to each world/GM to say what's actually available in it--the game should straight-out say that not every world is going to have every option.
Quadratic Wizards: Meh, I'd like magic to be both more magical and less powerful. Quadratic wizards, sure, but give non-magical ways of countering spells. Let you sacrifice your shield to protect you from a fireball, let you touch an illusion with cold iron to dispel it, let you counter a charm person with a blow to the head (I rewatched the first Avengers movie last night).
Grid/TotM Combat: Have it support both. If you have to use combat dimensions, then include the real-world dimensions as well.
Skill Challenges: I've never played 4e so I have no personal experience, but I've read a few things that suggested they were less than ideal at times. Like, it was far more likely for you to fail than to succeed, and even characters with no skills had to join in, thus making it even more unlikely to succeed.
Travel/Journey Rules: Very much yes. Level Up has some good stuff, although there are a few places that I think need improvement.
Social Rules/Social Combat: Also yes, as long as it details what can't be accomplished with social skills (no "I rolled a nat 20 and seduced the dragon" nonsense).
I have no real opinion on skills, saves, proficiency bonuses, or item creation, and my only opinion on feats is "as long as there isn't bloat."
XP: Story-based.
Templates for Monsters: I like 'em, as long as there isn't too much math involved.
Random Treasure Tables: Handy, boring, and unrealistic: Personally, I'd like treasure to be less common.
