Anyway, as for R&C now, just because the reimagining ended that way it doesn't mean that could couldn't still become a villain in the next one.
For example, GC reimagined could be set like this:
Qwark embarrased from the recent events disappear from the public. Then R&C get contracted to find the missing Protopet, which Qwark has stolen only to place it somewhere and find it himself and become a hero in a new galaxy. Once he sees that R&C came, he tries to send them back to Solana by impersonating mr Fizzwidget. He fails and the two find the Protopet and give it to him. He then changes his plan into releasing the protopet earlier. Then Angela becomes the Thief and escapes from the Megacorp facility along with the expirement in order to finish it herself or destroy it if she fails to. Although R&C get it back and securily hand it to Fizzwidget. Then the rest of the plot stays mostly the same.
I can't really see Qwark becoming the villain though.
Like at the end of both the movie and the game it's pretty clear he's a good guy, he's done some pretty bad things and has been rightfully punished for it but his heart is in the right place, so he's pretty much become his self from the Future games.
In the original game, while he wasn't clearly a villain, he hadn't been redeemed or shown any kind of development to the extent of that in the PS4 game so him still being a villain in the sequel made sense.