Thanks again! This is the kind of close look at the game's overall move potential that I am frankly not up for. I'm more open to replacing Gen 1–2 moves with better ones now than back in 2.2.0, since abilities have made the game so much more like a later-gen one anyway.
1. I'll probably replace Sky Attack with Brave Bird. Sky Attack's animation is too good to give up, but it works just as well for Brave Bird. (And I fixed those move effects.)
2. Aura Sphere is available for Blastoise, Togekiss, Mewtwo, Mew, Remoraid/Octillery, and Raikou. It's an improvement on Focus Blast that legendaries deserve, and it sets apart the few non-legends that get it.
3. Scratch and Tackle, like Fury Attack and Fury Swipes, are too different flavor-wise. I've already merged Spider Web and Mean Look, Detect and Protect, Mind Reader and Lock-On, Pound and Tackle, etc; too many mergers and all early Pokémon will feel the same move-wise.
4. Yes, critical hit moves were already in GSC.
5. If there were only one egg-based Pokémon I might remove Egg Bomb, but with two it's a neat move for flavor. At least it's not a TM. ;)
6. Color variation is based on DVs, so no.
7. Twister is learned by a lot of Pokémon, and it's the only low-tier Dragon-type move.
Here's a spreadsheet of the current move pool by type and damage, with special moves in italics and plain-damaging moves in gray:
Judging by that, Aqua Jet does look useful. I also really like the idea of an ability-suppressing move; not sure whether Gastro Acid or Worry Seed would be superior. (FWIW, I can more sensibly give Gastro Acid to Worry Seed users like Venusaur and Exeggutor than vice-versa.) The question is what to eliminate. Will think about it.
Edit: Okay, so current the current plan is to replace {Sky Attack, Twister, Egg Bomb, Haze, Morning Sun, Moonlight} with {Brave Bird, Aqua Jet, Skill Swap, Knock Off, Amnesia, Healing Light}. ("Healing Light" is a made-up name that combines Synthesis, Morning Sun, and Moonlight; I could try and give it a different animation for each user.)