Here and there
The story wasn't bad. It's starting to look like one of the old mario bros cartoon series or something. The humor was also decent. Considering most animators make jokes that are funny to them and not everyone else, this made me smile once or twice.
Now for the heavy hitter, The animation was poor. This looks like it was made with windows movie maker (which is a possiblility, considering you said you converted TO a flash video). Having characters jump around the screen instead of actually walking or running breaks the flow of the video, as showing lack of skill and makes you look lazy ("I'm not animating a training sequence"?).
It might have been from the conversion, but the text was choppy and a little hard to read at times, and I'm not talking about the already slightly difficult to read font style you chose.
Take a little time off to practice a bit of real animation, make the subtitles a little more legible, and maybe upgrade the graphics you use. (Don't draw a bunch of crappy craters, find a sprite of one from Metal Slug or something ;p). This could shape up to be a really nice series.