From a fan's point of view... Needs work.
Controls were a bit luggish for me, it might have been easier if you gave a control editor instead of given keys. Not only that, sprite styles were mixed, which is a big no-no, it would've been better to try using that 32-bit Light Armor X in the beginning. Enemies were limited, no replay value, and I spent five minutes with this one before I got bored. Story was also sounding like something I read from a fanfic a while ago, the fanfic I didn't like at all...
Nice touches I thought were the Light Armor X Mugshot, though recolored, and the endless loop from Zero's theme arrangement. Either than that... Not bad, but needs work, I suggest looking at MegaMan Zero Alpha, which was released by Flash Portal as well. (Ha, not breaking any promotion rules, it's related!) That one was a nice cleanup compared to this one, and the story is somewhat interelated to the Zero Series besides this one.