I haven't played Prime 3 or Other M, so I'll take your word on their contender status for most linear, but I can't imagine them being nearly as bad as I remember Fusion to be in that regard.
Like I said, I enjoyed Fusion, it's just not what I was looking for in a Metroid game. It wasn't a memorable game, really, and its attempt to infuse the game with story did it no favors. The cutscenes took me out of the game in almost every case. I don't think people really HATE Fusion. I think in the case of my argument, hate was a bad word to use. Dislike would've been better, but too late now, eh? Besides, Fusion's so old at this point that you're not going to see anyone really complain about it, and Other M kinda took Fusion's place as most disliked Metroid in the series.
I never really touched the Prime games. I played Prime 1 all the way through, tried to play Prime 2 and got turned off half-way through by the stupid plot. Didn't bother with Prime 3. I never touched Other M 'cause I don't have a Wii, but I have a friend who does, and has Other M, so I might well try it now just to formulate my own opinion about it.
I agree Prime 1 pulled it off well, but that's 'cause they segmented the silly story with long stretches of genuine gameplay and exploration, which I find genuinely amusing since Fusion kinda launched right alongside Prime 1, or close to it, right? I honestly can't recall. Either way, I think they let it get to their head with Prime 2. Anyway, I liked the Metroid games with a minimum of story. Anything more story-wise than Super Metroid's intro is too much for a Metroid game, in my honest opinion. So, I'll concede that I can't speak for everyone, but I think a lot of points people will agree with me on.
All I want is a Metroid game that tells me what I'm doing in the intro and then lets me tackle it any way I want and discover ways to deviate from the normal sequence of events. The games that don't are just a storytelling device pretending to be a Metroid game.
But, I'll agree this isn't really for this topic, so I guess I'm done here.