They are good at different things.
Personally, I think Super Metroid has better gameplay and music than the Metroid Prime. But in Metroid Prime, things could surprise you from the back, since you can't see all ways at the same time (which you can in 2D). It made me have a less jolly mood while playing. And that was great, I think.
2D - Classic. Great gameplay and bosses.
3D - Full of surprises.