In the next Metroid game, I can see the Federation being the antagonists. She defied orders in Fusion, and exposed their secret Metroid cloning program. I can picture her and Adam-bot running from them, and fighting the X.

Where did you hear this? Retro is working on Mario Kart 7 now.

Smash Bros? That's not a remake at all. It's a sequel. o_O

...Isn't Prime done? It's called a Trilogy for a reason, lol.
New Metroid game of course, but not a new Prime.

They all ready have four parts to the prime series (not much of a triology unless it's like hitch hikers guide to the galaxy), which inculdes metroid prime, metroid prime hunters, metroid prime 2 echos and metroid prime 3 corruption. They could be getting metroids from these planets Tallon IV (priate base) (prime), Aether (forget where but I remember them, though they might be dead because I think they were in the dark world) (prime 2) and they were on Elysia also (prime 3). We also have two plot points for them to build off of, no make it three, First we have who was following samus at the end of corruption (Slyux maybe?), then there is the kriken empire along with what happened to the other hunters form metroid prime hunters, then we have what happens after fusion. Oh and I also most forgot they could make a game to explain the origns of phaze and phazon.