My biggest fault with MP3 was the story. Not because of the VO, or the plentiful cutsceens, but because it intruded into the exploration too much. The AU or other random characters were constaintly telling you where to go. It ruined the exploration part because it was too easy. Sure, missiles and other optional power ups were well hidden, but with other items you always knew where to go.
The combat was too easy also. Hypermode is great, but i never felt the dread of faceing a non-boss enemy in MP3. I never died in my first play through (veteran), and on only two occasions in Hypermode.