I doubt he has multiple options like you think he did.
He almost never adds antagonists. It took him a long time to add Dark Samus and solely due to fan requests. He never even considered Ridley either till after Brawl(despite some requests). Why would he think of a far less important character over a more unique version of the protagonist? So no, I really don't think she had anything actually in her favor. She's definitely less unique than ZSS by virtue of one having a completely different set of abilities. Dark Samus, no matter how you cut it, is a variation of regular Samus' abilities. She's basically her Akuma, and still based off of the same concept of abilities.
I get wanting a unique Dark Samus too. I'd like that too. She has way more potential. Doesn't mean she was actually on the table either.
Keep in mind the first character he added for the sake of being an antagonist alone was Piranha Plant. Bowser was constantly active as not just an antagonist and part of the main Mario ensemble. PP was literally added cause he wanted someone who wasn't a protagonist. Not even Ganondorf was added for more villains, but because he worked out as a clone and had some requests. When you have characters like King Dedede and Meta Knight, they were only borderline antagonists and often on the hero side in most cases, or not even being remotely evil in the actual canon games. So of course they were thought of first. Coupled with, again, Metroid doing poorly in Japan, his choices were still limited. The gimmick is probably what pushed ZSS over the edge of others if he even thought of others. He's very rarely done clones that are the same person as is(with literally Dr. Mario being the sole one, and he wasn't received that well anyway). So Fusion Suit Samus was probably not on the table either, at least before a completely unique version of Samus who also plays an important role in the story, the fact that Samus is still a human underneath, something that you actually are trying to unlock via an ending quite often. Still better than the bikini design, despite obviously a fanserivecy design.