Well the story presents Samus as the dumbest person alive. She suffers third degree burns while she could just activate her Varia suit.
Other than that, the way you use missiles is horrible, the game is much more linear than other Metroid games. There's other stuff but they've been blocked out of my memory.
I think they tried to make too many Wii games too causal and accessible that they missed the point in some of the games, you obsolutely can't dumb down a Metroid game.