My opinion: biggest problem is the complete lack of any subtlety in the script and direction. I mean, Wily was a great actor, but the way his intro scene was scripted, he might as well have just looked into the camera and said "hi, I'm Dr. Wily, and I'm the villain of this movie."
Granted, we know he's the bad guy, but still a bit more depth and subtlety in the writing could have made this movie a lot better.