I like all of the 2D metroid games, but I've never really been big on the metroid prime games. They are fun, but I find the ingame puzzles a bit tricky and distracting. I also don't like the fact that you have to scan everything in sight if you wanna understand what's going on in the game. On top of that, The worlds and enviroments that you fight in are a bit too eerie for my tastes. It doesn't help that in the first metroid game metroids start breaking through glass in a pitch dark room and try to attack you.
I probably would end up liking the games more if i didn't suck at them. It seems that with every game I play I get stuck at least once. If I don't get stuck in a game it's because I have a strategy guide.