Off the top of my head:
- You control Samus from a 3rd person perspective in a 3D environment by holding the Wii-mote horizontally like an NES controller. Try to imagine how much of a pain it is to move correctly in 3D space with just a D-pad.
- Until you have to shoot missiles, in which case you point the Wiimote at the screen to enter first-person mode, but now you can't move until you hold the Wiimote horizontally again. Which is a pity because the first person mode looks and controls well. You can imagine how this might open you up to take damage when trying to switch between control schemes while trying to blast a boss with missiles.
- Occasionally the game will just stop in the middle of a cutscenes and force you to play I Spy with the Wii-mote so that Samus can identify some interesting detail and point it out to the other characters to continue the story. I distinctly remember one of these being a pile of green puke on top of some already green grass, almost invisible.
- The story is full of a lot of repetitive dialogue that overly-explains what a character is feeling, or summarizes story events that literally just happened five minutes ago. There was also a side plot where one of the Federation Soldiers Samus is with is secretly evil and killing everyone else off. I don't remember if they ever revealed who that was or why he was killing everyone off. I think maybe he wanted to steal the secrets of making Metroids and sell them off to the highest bidder?
Overall, easily the worst Metroid I've played, and I personally think it's the reason Nintendo put the franchise on ice for almost a decade.