Here is my thoughts on Metroid Prime 2 (Just to note: I am only about half way through Prime (Grav suit) and Fusion (Speed boost), but I have won the rest of the games)
USE THE BROADBAND ADAPTER!
Yes, I know that it may ruin the continuity, BUT not if it was a big part of the game. Yes, Samus works alone, but I can't imagine that she is the ONLY bounty hunter. (I SEVERELY doubt she is the ONLY one in the Galaxy that even has her suit or ship) Heck, maybe even have a rival in the game (Like Sa-X), but out for the bounty. Maybe work together occasionally, maybe try and stop the other from suceeding, and just for fun, a multiplayer Deathmatch variant of the game.
Hmm... Metroid Pime LIVE. Take the whole planetary system, allow travel between the planets, have the game moderators throw in troubling stuff at random, choice of massively multiplayer or single player (single player campain can allow the multiplayer events to have effects in the single player game)
Speech. Not too much, but more little things. Samus talking to herself, intercepted radio signals, pirates chatting, etc.
Level Editor! (Save to your memory card)
Let me fly her SWEET little space ship! (Fly it to other parts of the planet, or even fight Prime in the air!)
LMSx has a good idea with the uplink, but I say take it a bit further: When in serious trouble, call in a sub-orbital strike from her ship.
Ooh! Cloak abilty! Flight pack! Buzzsaw Morph Ball! Deformable terrain! Zero-G combat!
Imagine a MMRPG version of Prime with all of the above: At least one planet would be a complete wasteland because of a massive number of people playing, fightinh, and just blowing the h311 out of the place.
Also, with how many times she has lost her abilities due to little things (Radiation spike, viral invasion), why doesn't she make a backup of her abilities software and have someone try to reverse-engineer her armor and weapons, you know, just incase.