Well, some of them deservedly so.
I played
Federation Force recently. Call me stupid, but for what its purpose is I don't think it's a bad game.
Clearly it's one of the worst games in the franchise, but it's just a mission-based multiplayer game with a Metroid feeling and it's kinda entertaining if played with other people. Then I think we can all agree that it was release in the worst moment possible for Metroid, but it's still part of the series and Prime 4 will probably be based on the events of Federation Force.
Now let's talk about
Other M: I think it's a decent game overall and a mediocre Metroid game. Still, I believe it receives too much undeserved hate.
I won't discuss the gameplay, but the story has two main problems:
1) It focuses more on a character's psychology, behaviour and relationship with other characters rather than the actual events and it is written by Japanese for Japanese. We know that Japanese people sometimes, in some situations, behave in a way that we westerners perceive as a "weird" and not always we are able to understand it.
2) The game has literally been massacred outside Japan by the localization team. There are a lot of missing or modified elements that mess up characters, dialogues, the worldbuilding and more.
I highly recommend watching this video, where a guy fluent in Japanese language analyzed the game's dialogues and pointed out the most important differences between the Japanese version and all the others. Maybe it won't change your mind about the game, but hopefully it will at least make you aware that the story you experienced is only partially the actual story and that a bad localization and translation can completely change the perception of a game.
With that in mind Other M doesn't magically become an amazing game of course, but a lot of unclear points are now explained and it is definitely improved, overall. I hope that someone felt the same after watching this video essay.
In the end, I don't think a bad Metroid game exists. Some are amazing, some are good, some are mediocre, but there aren't bad games in the franchise.