Hmm... OK then
Well, you seem to have Flash down pretty well, the animation looked pretty damn smooth and everything. Obviously being too short is the downfall, and there are a few inconsistencies:
1- The first scene says "4000 AD" yet the Megaman Zero universe is supposed to be set in 22XX (or possibly 23XX if you believe that MMX Command Mission is in 22XX). That would mean Zero is almost 2000 years old in your story.
2- For a prologue, very little is really explained. Why is Zero in the desert for example? But then, as your author comments say, you don't really have any real idea for a plot yet.
3- What is the reason for his revenge? We see a scene where he's just about to fight an X Clone, then it cuts out.
I'm not too sure about ideas for a plot. Perhaps Omega X and his army has attacked and destroyed HQ. Zero clashes with Omega, but fails, and is now searching for any clues that may help him in gaining enough power to defeat him. Not sure though. Try looking at some other Megaman-based flashes for inspiration such as Megaman X Gets Taxed, Megaman Polarity or any of the flashes by CheveLoco if you haven't already.
You have the skill, so I'd like to see it put to use. I'll keep an eye out for your work.