Best, I will just have to say Zero Mission. Perfecting everything Super and the Handhelds ever tried to do. With solid Sprite gameplay, Exploration and replayability all into one of the best games ever made. However, that doesn't make it my favorite, which goes to Metroid II: Return of Samus. Mostly due to countless hours of Nostalgia, trying to get the best time (1:07) and the fact that its the only game where you've truly been out to fight the Metroids and fight for your survival.
The only one I can say I don't really like is Metroid Prime 2. Its just too much backtracking. Way too many randomly placed doors. The whole Light/Dark world Setup striked me as a little familiar (Zelda anyone). And after the original Prime, I was getting fed up with having to struggle more with a 3D map and find my way through areas I had already been more than fighting anything or progressing through the game. A game shouldn't take 50 hours because of trying to find a door. Metroid games usually are about running into a room, seeing immediately what you need to do and, if that fails, trying your arsenal of bombs or Missiles. In other words, VERY well designed areas and puzzles. Not having to struggle with a 3D map and various dimensions.
Six upcoming games you should look into:
