We're kicking this list off with the two games that tend to frequent most player's least favorite Metroid games, Metroid II and Other M. There's really not a Metroid game I don't like, it's just that there were certain things these games did right and, well, some things they didn't.
SPOILERS FOR BOTH GAMES TO FOLLOW!!!!
My biggest problem with this game (as well as the original Metroid) was that it was extremely easy to get lost, and the game has no map to help you get your bearings. While this does help attribute to the feeling of isolation that Metroid likes to bring, it would have been a nice touch. Again, this game is not bad by any means, I just enjoy the others better.
This could all change if they would remake it! Check out AM2R (Another Metroid 2 Remake) on YouTube; this is what we need!
As for Other M, I feel this game is a lot better than most folks give it credit for. While I was a little weirded out hearing Samus being so chatty, I attributed it to the fact that the gameplay to story ratio for video games has changed so much in the past decade or so.
That being said, I too was a little shocked to see Samus react so strongly to Ridley's presence as opposed to her usual calm demeanor, but in her defense, we all thought he was DEAD. And not just Nintendo dead, the guy's remains were on a planet that was soon after completely vaporized! I'd be surprised too.
The 3-D implementation of items like the Screw Attack and Speed Booster were amazing! It was like playing a remade Super Metroid, so my complaints about this game are few.
I did find it strange that they really seem to downplay the Chozo's contribution to raising Samus. They are the ones who made her who she is, after all, and it just felt out of place for them to almost completely discount them.
To end on a positive note, this game has a ton of homages to other games in the franchise, so it was a real nostalgia rush for a fan like myself. I'll have to play through this one again soon!