Since three of the four options in the poll sucked, I said make it more longer and challenging. I know that is pretty much standard fare in a sequel, but none of the other options will really add to the Metroid world.
Multiplayer, in the style of fragfests, would actually degrade Prime. Nintendo has stated that the game is a FPA, not an FPS. Unless Retro could think up of some clever way to install multiplayer that uses the core elements of the series (much as how Zelda: The Four Swords did), then it wouldn't be such a bad option. However, I doubt the GCN can handle co-op with Prime's lively environment.
I don't see much for the GBA-GC connection. The furthest Retro could go with that idea is probably Nintendo's way in the Wind Waker. A friend will play as a helpful character (Adam, anyone?) and will help the friend who is actually playing Prime through the journey. Even if that is implemented, that still would not be such a big option. I don't hear many people talking about the Tingle connectivity in Wind Waker.
2D perspective? This is probably the second-best choice in the poll. I would not mind this option, but sales of MP2 will then be poor and, as many people have stated, this is better on the GBA.
In my personal opinion, I would like to have the controls changed as well. Miyamoto's setup was a good idea, but it proved to be uncomfortable at times. I remember fighting Flaahgra and taking unneccesary damage due to the awkward control setup. I was unable to evade Flaahgra's bitch-ass tentacles and that almost screwed me over a couple times. Believe it or not, I think it would be better if the FPS setup was adopted the game. That way, I could walk and look around as well as fight enemies a little easier.
Still though, it is bound to be great. Even if the game is a rehashed version of Prime, it would still remain one of the best titles in the GCN library.
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