If the Galactic Federation can upload the minds of great leaders such as Adam Malkovich (lol), I don't see why the Space Pirates can't have the mind of Ridley uploaded. Give him some sort of "body" for now, whether it be its own entity or within a complex computer network. Then find away to restore his actual body.
The Space Pirates themselves don't need much of an excuse; The entire organization wasn't based on Zebes, so they can easily make a return.
Heck, here's a somewhat silly idea: Call it the "Ridley strain" or something like that. Have a certain lone Space Pirate start to act funny. He then starts to deviate from the behaviors of other Space Pirates, becoming more and more independent, crazier, and more violent. At some point he starts to feed off of other creatures, and at another point gets his hands on human flesh. Eventually he undergoes a transformation and.... "I'M BAAAAAACK!!!"
That reminds me, it would have been more interesting if "Birdie" Ridley wasn't actually some larva state but rather an amalgamation of various creature DNA that only managed to become a living entity because it carried Ridley's DNA. What then happened was not some goofy metamorphosis from cute fuzzy cat-chick to the Ridley we all (almost) know, but rather Ridley's dominant DNA violently overtaking the body to the point where it was capable of undergoing extreme physical changes in order to regain as close to its original form as possible. That could also explain why Other M Ridley was so ugly and unlike its previous look. It's Ridley, but with traces of other creature DNA remaining so that the resemblance wasn't 100%. Heck, maybe Samus's very appearance triggered the change. The creature was relatively docile, and for a moment it didn't recognize Samus, henceforth the initial lack of a reaction. It took a moment, but something primal and deep within triggered, which is why when Samus took another look at the creature, its cute clumsy demeanor had vanished and was replaced with a sinister glare, as if the creature was thinking "...I... know you...".
...But yeah... =/