I love both the 2D and the 3D Metroid games. But the 2D ones, are the better games in the series, despite Metroid Prime being so spectacular. That's just how freaking awesome the Metroid series is; even the "lesser" games in the series are amazing.
I think Metroid deserves the full-blown 2D console release treatment like Mario and Donkey have been enjoying. (And a 2D console Zelda, for that matter.)