I think a reboot would be a colossal waste of potential of what they could be doing post-Fusion. Samus could be on a missions from someone OTHER than the Federation. The Fed could be hunting her. The key would be interspersing that stuff as small breaks in the otherwise brooding exploration aspect. I would say just do what Star Wars has done: throw out the junk (mainly Other M and the connecting tissue) and keep only the good. Classic and Prime make cannon. Bam you've whittled out the serious garbage.
But I agree with what you say on some things. Iwould personally love a prime style trilogy where the Fed is in civil war following the events of Fusion and Samus gets sucked into *some* of that but ultimately is mostly doing her own thing. Maybe some bad stuff is happening and the Fed isn't paying attention because of the War and Samus is looking for it. Also, I could see her Fusion suit degrading if it is repairable only through Fed tech which she will no longer have access to so for part of the trilogy her suit is degrading and you get some weapons that are almost jerry rigged (some new weapons) and then later she makes contact with the Chozo in the course of her investigation after her suit has degraded to dang near useless and she gets her classic varia suit back. Would be a nice spiritual reboot, bringing the series full circle back to Samus as a more independent bounty hunter/hero. I should really write this whole thing down somewhere. Plus I think "loyalty" is a better internal conflict for Samus than Other M's stupid daddy issues.