Well, first and foremost, get a preloader. They are not hard to put in a flash. No matter how short the flash is, nobody likes a white screen waiting for it to load. You can easily get them from the downloads section.
Second, there was way too much standing around for samus. At the beginning she was moving around too much, then she stopped moving for half a minute when she should have been sniping crazy hand. And what was wrong with using Zero mission/super metroid sprites or using metroid fusion samus? Any particular reason you picked a custom sprite that seemed to have limited poses?
Anyway, the actual fighting seems okay, you just have to work on movement mostly.
this is freaken awesome nice job im a fan of ssbb where you get the sprites and background from?
Google and Sprites resources
nice quality, excellent animation, but is a little short.