Not everyone is aware that there is little to no functional difference between Samus and Dark Samus. I remember there was some shoddy article on a site rating the Ultimate characters from best to worst, and it said that Dark Samus was more powerful than Samus, but didn't specify how. People who aren't very informed about the deeper levels of the game can easily mistake differences between the two that don't exist, not understanding that Dark Samus and other Echo Fighters aren't the same as clones, which isn't made any more intuitive due to Ken.
When we were analyzing pre-release footage here, there was a lot of debate as to what differences there might be, because just from sight without hands on the controller to easily compare, it was hard to tell. For example, one piece of footage used for Dark Samus was her using bombs to squeeze through a gap in Morph Ball form, which caused many people (including pros like ESAM) to jump to the conclusion that her bombs/Morph Ball had more horizontal movement than Samus, which was just flat out wrong.
Things were made even unclearer when the official Super Smash blog did its Dark Samus post and said "With floatier movement, she's a little different from Samus," which sparked discussion as to whether or not she genuinely had different movement attributes from Samus. After some analysis and debate, it was settled that the post was either in error or just referring to the characteristics of Dark Samus's animations, not her actual physics (e.g. her animations make her appear floatier, but in actuality she's the same weight as Samus), which turned out to be true in the final game. But it's not likely that everyone got the memo.
The aesthetic factor is a major part of it, though. Samus's design in Smash 4/Ultimate isn't exactly her most popular, whereas Dark Samus is one of the best-looking fighters in the game, with a lot of work put into her model, effects, and animations. I saw a lot of reactions from people who don't care about Metroid and have never played it once in their life, and when they saw Dark Samus they were immediately drawn into her appearance and her animations, despite not knowing who the character was or caring about the series at all, and some even said they'd try and play her. Perhaps some of those people ended up maining her.
Me, I'd been waiting 14-15 years for Dark Samus to join Smash, so she was my main from the second she was announced. Samus was only my tertiary in Smash 4, behind R.O.B. and Dedede.
