1, 2, 3, 4, I see plot holes, look, one more!
1. When was the last time anyone saw Megaman PRAYING?
2. When did Mega get a shuriken/ninja star/whatchamacallit?
3. Personally- just an opinion- The main villain could have at least gone out with an ending line, like, "This can't be happening! NOOOOOO!" or something like that. It adds a nice, fresh cliche to the end.
4. Aren't the darkness clouds supposed to be called program corruptions or something?
5. Why is Wily just sitting by while one of his most important programs is destroyed?
Final note: Seeing as you don't take to rudeness very well, I'll end by apologizing for mocking your hard work. You obviously put some time and effort into this, and I respect that. Keep it up.