The best part of Metroid's timeline is how simple it is to make Metroid games that have zero to do with it. It's too bad that Nintendo doesn't seem to understand that (well, Retro understood).
Samus is a bounty hunter and she isn't as bound to the history of the world of Metroid as Link and Zelda is to their world. The only thing you need to figure out is the reason for there being metroids in the game and you're set. And considering that those flying jellyfishies are spreading throughout the galaxy faster than the zerg thanks to space pirates, scientists etc. that shouldn't be a problem.
I guess another problem would be the suit upgrades. A simple solution to that would be upgrades specific to the worlds Samus visits. Once Samus leaves the place she loses her upgrades and you won't ever need to use that damn authorization fix for the next game because Samus already comes equipped with enough weaponry to blow up the moon. This solution would also make every Metroid game more unique in terms of upgrades, environments, enemies etc.
We've already mastered the basic upgrades such as missiles, bombs, grapple beam etc. so those should be enabled from the beginning. I want the designers to come up with new equipment instead of making me search for the missile for the nth time. This goes for Zelda as well. No more knowing beforehand what atleast 4/5 of the upgrades will consist of.
