I've gotta say Speed Booster/Shinespark. Now, if only Retro could figure out a way to put that in MP [insert number here]
Speed Booster might make it into the next one,; that would be pretty cool. I doubt the Shinespark will ever be in a Prime game, but maybe they will try to include it in a Metroid game for Nintendo's next next-gen console. It would probably be hard to do, but it would be worth it, IMO.