Ooh, that'd be a cool one even without the crossover element...

Though if that's how it goes... Maybe subvert the Metroidvania conventions: Samus starts with everything she had at the end of Dread and doesn't lose it. Inexplicably, in fact, it all starts getting stronger because Ridley's genes have activated in Samus's gestalt and, since the power suit is part of her body post-fusion, its regen is being augmented by his and kicks into overdrive: In short, her "physical amnesia" is cured and previous bits of technology, biology, or other that had previously been incorporated into her suit end up recreated which due to slight differences in versions of each it results in an overall improvement to the desing as it manifests.

At first, Samus thinks to herself "this is fine. You know, it's a good thing. Ridley owes me this after all the **** he's done" but the worry that other, less beneficial traits could manifest in the future just, you know, it gets to her when she stops to breathe...

But also, um... The threats on this mission are something she's never seen before. Even those upgrades aren't enough, so much like going Phazon Mode in the Prime Games Samus has to periodically tap into her Meroid powers to unleash the mega bull**** laser. This is fine, she's in control, and it's only for a few moments at a time.

...and then, and then... The regeneration recreates the Phazon Suit. There's no Phazon for it to protect her from or channel, not anymore, but it's there. And when she goes Metroid Mode after unlocking that upgrade she catches her on reflection and a Phazon Suit Ultimate Metroid... Would look an awful lot like Dark Samus.