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"In general a post fusion game is a post Metroids game."
I dunno, all you need is one Metroid (or apparently one scrap of a Metroid's DNA) to create a million of them, and I do not recall any indication that the BSL was the only facility with samples like that. Even if Samus remembers Other M and washes off the Omega gunk she got on her suit in the final battle of Fusion, there are relatively easy ways to write standard Metroids back into existence.
Heck, FF just straight-up says, 'Here's a Metroid. Yeah, we have no idea where it came from. [chibi shrug-emoticon]'
I kind of appreciate the lack of pretense, haha.
"Also the Space Pirate Confederation seems weakened and in that sense I do get why it's hard to come with a new main baddie (especially since Nintendo usually oneshots new villains in their main franchises)"
Huge spoilers for Samus Returns's 100% completion ending:
Given that they (for the most part) have been portrayed as way less inept than the Federation or the Pirates, I look forward to that.
"At this point I could see Ridley coming back as an alien ghost, seems like the next proper contrivance they could use, is not like this franchise hasn't had ghosts."
That is actually a pretty good idea.
"The Metroid Prime did take Samus skills as well as creating Phazon, from wherever that thing came from."
Yeah, and in the original (superior) version of the game, there were logs detailing how it also absorbed a bunch of Pirate Troopers and their technology, which is why the first form has the various beam immunities and a bunch of obviously-mechanical parts (that make no sense with the explanation Corruption tries to give).