There are FAR too many of those.

All the beams and visors, bar power, combat and scan only appeared in Metroid Prime 2, for example.

Though if you're talking selectable abilities in that you can turn them on and off from the menu, that's just Super Metroid, and the only item from Super Metroid that hasn't reappeared is the Reserve Tank, which can be auto or selectable from the game itself, so really, too many options.