Good, but here's what you can do better.
Story-wise, I enjoyed this quite well, though some things did not add up at times.
-Bass' dissapearance was dissapointing.
-Sprite styles from different series were mixed. BAD!
-The 'Federation' was too Trekkie, if you know what I mean.
-Mega Man may've had a child personality, but he was never a coward, unless this is some kind of battle strategy for the next episode.
On a good note, the use of music from different sources other than Rockman/MegaMan stuff was enlightening, I might download a couple of those different tracks.
All in all, make sure not to mix sprite styles for episode two. You can find a custom 32-bit Shadowman full sheet, as well as a full custom 32-bit Protoman sheet. I can get ahold of both of those if you're interested.