It's a lot of things, really. The biggest is the difference in marketing. Steam got almost no push.
But I think it runs deeper than that. The game is really ugly, which is just unappealing when that's the first thing you see. It's one of the ugliest games on the system. The art style was a misstep as well. It was a bad idea going with a comic book aesthetic without understanding why people like to read comics in the first place. The shallow narrative didn't at all match the art direction.
This goes back to a huge problem with Nintendo, which is that they never hire competent writers for this kind of stuff. Steam needed a deep and compelling narrative, but had a Mario/Zelda-tier plot. It seems like the only reason they chose the comic art style was because it made for a neat way to animate cutscenes, instead of because they wanted to tell a comic-esque narrative.
Steam could have been Nintendo's Justice League or Avengers, but now it's just a shallow SRPG with ugly graphics. Hopefully they'll give the IP another chance and fix all these things. Likely not, though.