The Metroid series is quite simply fantastic. It's my all-time favorite game series, mainly because it features my all-time favorite style of video game gameplay, exploration based platforming.
Although I could never get in to the original NES Metroid, I still think Metroid II is an incredibly fine title. It's not for everyone, but I still thoroughly enjoy it. Super Metroid deserves a spot on the top 10 greatest games of all time list in my book, just because it captures exploration-based platforming like no other game has ever done. Zero Mission and Fusion are awesome games that I emulate and play through even today.
The Prime series is also fantastic. The later two may not be everyone's cup of tea, but I've yet to find anyone who truly thought the first one was a bad game or a step in the wrong direction. Again, exloration-based FPS at its absolute finest.
Other M is where people either drink the cool-aid and go with popular opinion, or they just hate because of the story and execution. The concerns are warranted, but I don't think Other M is a bad game, and I don't think it's the worst thing to every happen to gaming ever (those who think the latter truly do annoy me). Yes, it had quite a few steps in the wrong direction, but it could have been a true series-killer such as Sonic 06.
All in all, one of gaming's greatest franchises for sure. I'm really hoping we get another in the near future.