It should be noted that while even though Metroid Prime did outsell Super Metroid the Prime sequels did not fair so well. If Prime was a superior game you would think sales of Echoes and Corruption would have been at least equally as good, but they aren't. This means a lot of people who bought Prime were not pleased enough with it to bother with the sequels.
I really hate that the backspace key wipes out all progress and sends you back a screen...retyping this all over again...
Or maybe people saw Echoes for the tedious, sadistic chore that it was and were cautious about buying it, an effect that trickled down to Corruption later on. I do think that Corruption is a more fun and more interesting game than Super Metroid, but I can accept your argument for why you think Super Metroid is the better game.
If you want to bring up the sequels, though, I'll bring up Metroid: Other M, a game
specifically designed to be the successor to Super Metroid in terms of story and gameplay. That wasn't received so well, was it? And yes, I know there are many deserved reasons for that, but you wanted to bring up the sequels for some reason.
EDIT: And I hate the "better" argument with these two games myself, Insanolord. I just hate seeing Super Metroid put up on such a (nostalgia-dominated) pedestal by so many people, as if it's automatic that Retro couldn't create anything of equal quality. That's why I left it labeled as "food for thought".