I like Fusion and Zero Mission.
Why? I mean Fusion is pretty linear until the very end where you can finally go around a bit freely searching for items. But the story is so exegaratingly "tense" and samus talks and there are doors locked behind you so you need to hear a "briefing".
The difficulty is very unbalanced too, its very easy at first and once you have to face SA-X it gets sometimes ridiculously hard.
Tbh this game is so un-metroid like of them all because of that.
As for Zero mission, I do find it better than Fusion but it has some poor retconning stuff in place, while I like certain areas/stuff, I understand why many old Metroid fans hate this game so much. I see it as alternative retelling of story more or less. The stealth part after the original game part rather pissed me off at first though, but now I do appreciate it for being different but it's still not very well done imo.
As for my own favorites, Metroid II takes the place from the old 2d games (wish the proper gameboy color port was originally released though instead of not being released), simply because it is very dynamic, even though it's far more linear than the original game and it centers a lot on the metroids themselves for a change. Metroid Prime comes as favorite of the 3d games I guess but I still have to properly finish it (don't have acess to gamecube all the time, haven't had for some time now). Metroid Prime Hunters surprised me a bit, in both positive and negative sense. It seems to me that if it actually followed the main story it would be better conclusion than what they made the "trilogy" of, except that the story for hunters was made to strip off the stuff and make it more of a spinoff story not tackling into phazon at all or even metroids aside some references in the final version. I can see that some elements from the original metroid prime 2 pitch went into this as well, despite not being primarily
developed by retro. However the good things about this game is that once again it allows you to do more stuff out of order, this time even with bosses (though its clear that you do them out of order and they will also be more difficult). But it offers you more choice of path than all of the other modern metroid games. And it is more action paced and dynamic again. The bad thing is that some boss fights are really irritating and some areas like the piston cave which I almost thought that John Romero in his Daikatana time would think of something so unfair as that. And of course there's the multiplayer(for me just with bots, but at least this option is there) and it keeps it from eing boring/monotonous simply by it not having forced to split screen and because you can play there as the other hunters/characters which all have some special skills/abilities. The game even has two very different endings to begin with and you can skip a boss fight too. Even though the story ends up more or less like rehash of the
original only this time with "artifacts in artifacts". I also don't know how nobody could spot the obvious reference with the gamma radiation as well and the fact that the final weapon/beam has a metroid shaped symbol on it to begin with. Some stuff in the game might not make sense at first, but on second look it's brilliant. I thought the escape sequences meant the planet or something was going to blow up, but the point is that it's the security protocol in the octolith tht becomes part of your suit and if you don't make it to adjust it at your ship/terminate this process, then it's simply game over for you. That's at least how I began to understand it, sort of like kill switch thing.