Prime 2 is the best btw. :p
Love the narrative, graphics, atmosphere and gameplay of that game so much! Some of the bosses are annoying, but most of them are much better than those in Prime 1. And it has the screw attack!
A bigger, better, more ambitious and harder sequel. The fetch quest near the end wasn't as bad as most people make it sound, imo it's much better and easier than the one from the first game, some keys were hidden very cryptical. I also hear a lot of complaints about the backtracking, but ignoring the final fetch quest (which the first game also has) you only need to backtrack twice: once for the seeker missiles and once for the power bomb upgrade. Also, let's be honest, Sanctuary Fortress is the coolest looking place in the entire Metroid franchise.
Best 2D Metroid game is easily Fusion for me. Great narrative, amazing atmosphere and pacing, best villain in a Metroid game and contrary to popular believe, there is exploration in this game!