I still want a game after Fusion. After all, Samus just blew a federation conspiracy and space station sky high, with the help of a military mind which knows many secrets of the federation, They arent going to be exactly happy with her. Actually, they are most likely going to try to kill her.
Some would, some wouldn't.
Assuming the likes of Keaton (read the manga, boys and girls, its canon) are still in charge, Samus still would likely have more than a couple of people who would be ready to be at her aid, even if some generic, "corrupted military personnel" are after her hide. Probably in interest of keeping her alive, because of the Metroid in DNA, if nothing else.
What I think would be interesting to see, though, is if she may be forced to make some rather interesting partners as a result of her being forced on the run. Imagine if things worked out, such that she and Ridley are forced to work together, for instance!