Ridley and Dark Smaus would both be good characters.
Rundas, Ghor, and Gandrayda would all like a word. The bounty hunters in Metroid Prime Hunters were designed to be like Samus, but bounty hunters in Prime 3 were NPCs and bosses so there was much more liberty for them be unique characters.
I'd love to have Rundas since there aren't many ice elemental characters aside from... Oh wait, there was only one ice elemental character(s) and that was the Ice Climbers. Rundas would be a more bulky, defensive character compared to Samus so, he'd be the Ike or Ganondorf to Samus.
Gandrayda's weird since she's a shapeshifter with electric powers. Hmm, I guess all of her attacks could be based on different Metroid characters. In a way, she'd be the "cloniest" character since she'd have no "original" moves even if those moves were never seen in SSB, but in Prime 3. Also, she'd be like a summoner character who "summons" to attack and she'd be a bit like Mega Man who uses other people's powers alongside hers.
Ghor would literally be Little Mac in terms of normal and Final Smash gameplay. For starters, normally, he'd be this lanky cyborg who could be the speed character of Metroid. When he uses his Final Smash, he'd put on armor and go to town on people at the cost of speed and having a much larger hitbox.
The only issue is that Metroid only has 1 protagonist, Samus, 2 recurring enemies, Ridley and Dark Samus, and 1 very well-known boss, Mother Brain. After that, you have your generic enemies, generic NPCs, and one-shot characters who are one-hitter-quitters since almost all of them never return for another game or outright die in their single appearance.
Well, we could just pretend "Samus" is SA-X and Zero Suit Samus is the real Samus and call it a day. Hey look! 2 Metroid characters who aren't clones like the Star Fox, Zelda, Mario, Mother/EarthBound, and Fire Emblem characters.