Super Metroid is, of course, the game that almost all the older gamers will say was the best of the series. I think I mostly agree with them; it was the biggest, prettiest and most elaborate Metroid game of the older generation. All the places you could go were nicely decorated with actual backgrounds and had interesting stories (if that makes sense), enemies were more detailed, and there were plenty of new and interesting power-ups to find. Don't get me wrong, though. I liked the original, and I liked Metroid II as well. Seeing the graphical leap from those games into Super Metroid is certainly a contributing factor to its greatness, though. I think the thing I liked the most about Super Metroid was the way the game portrayed you in such an absolutely desolate world. The atmosphere of the game, I mean. Almost every living creature on Zebes would try to kill you on sight, so you were really on your own there.
The jump to 3D with Prime I thought was pretty good. It had a similar atmosphere. You were a lone hunter on this whole new planet and you were on your own. The power-ups and all were also cool. Metroid Prime 2 was also pretty good in its own right, in my opinion. I liked the new weapons and visors, as well as the expanded world of Aether. I think Metroid Prime 3 was where it started to fall for me. The Wii controls were cool and all, don't get me wrong, but it kind of started to lose what made it Metroid in the first place there.
Now, with the advent of Other M, I hear a lot of rather disappointing things about it. I haven't played it yet, so I can't say much. All I can say is that, so far, my favorite "era" of Metroid was between Super Metroid and Prime 1 and 2.