I thought everybody's beef with Other M was mainly story
The biggest problem is definitely the story, but that's only because the story is so so so so bad, the gameplay is definitely below average aswell.
First things first, the controller is a serious issue. Holding the Wiimote sideways was never very comfortable, even NES controllers feel better than that, but having to control a character in a 3D space with a D-Pad is just a design sin. Of course they chose that control option so you could seamlessly switch between the 3rd and 1st person perspectives, but the 1st person perspective is never used in an interesting enough way to make up for the faults that the controller choice brought with it. In general it just comes off as confused and lacking of any real identity in that regard, sometimes it's 3rd person from a bird's eye perspective, other times it's 3rd person over the shoulder, then it's suddenly a 2D sidescroller, and then you have to go to 1st person perspective, none of them are properly fleshed out or feel good at all, it tries to do everything at once and then ends up doing none of them well.
Speaking of the 1st person perspective, you have these moments throughout the game where you can't move and have to point your crosshair at a point of interest, and by god they're awful. You're stuck there until you figure out what the **** you're supposed to point at, which is often very hard to see as the targets are sometimes really small and the Wii was still stuck in the past generation in terms of resolution, so you basically end up just flinging your cursor around just hoping to get lucky. They're probably the worst sequences in any big budget Nintendo game ever, I have no idea who thought that Find Waldo had any place in a Metroid game, or any ambitious game at all for that matter.
The combat itself is also incredibly shallow, once you get down how you dodge you're basically invincible. For the most part the gameplay just goes charge shot -> dodge -> charge shot -> dodge, etc. There are also these cinematic sequences, and although they can be cool to trigger they're basically just cutscenes you mash through, they just don't feel interactive at all, they could have taken a leaf out of Resident Evil's book in this regard.
The game is also absurdly linear, and upgrades are extremely weak in this game aswell, so it just feels like any exploration is being discouraged, and any upgrades beyond Energy and Missile Tanks are locked behind story progress iirc, so no sequence breaking either. I know it was trying to do something different, but come on, you don't do that stuff to a Metroid game, might aswell make it a new IP at that point.
There are also a bunch of other minor gripes I have with it (stop forcing me to walk slowly through corridors ffs), but overall the gameplay still isn't worst game of all time level, it's more that for a AAA Nintendo game it's incredibly disappointing, and when you then combine that with the awful awful awful awful story you ultimately get a truly miserable experience. I might be off on one or two details here as I last played it 8 years ago, but you get the gist of my complaints.