It's probably because she shoots while running otherwise if the arm bounced the bullets would be at different heights.  And that would be a bit confusing for players if it did.

I have one small complaint to this othervise good pix. The dark blue line on her helmet seems kinda jagged. Unless there is some specific reason for this you should smoothen it a bit. I've made an edit how it could be done. http://i7.photobucket.com/albums/y291/flarfy/MegaGirl.png

The animation of the legs is okay, but as have been said, could benefit from being a bit different.

 I agree with shibumi about the arms.

I'd like to see the gun arm bounce vertically a pixel or so during the run cycle. It only moves horizontally,  as if it's being supported by something very rigid. Very nice rotation on the head and body.

Yeah, just checked the frames. The legs do look the same. The leg in the rear could benefit from a little more shading. Oh, and technically this is a brisk walk.  When you run, there's at least one moment where both legs don't touch the ground.

Anyways, love the character and the upper body motion. =)

This is a great character, and I'm very impressed at the dedication needed to make an entire game - best of luck to you.

Just one thing on this running animation, though:  The impression of the animation is a decent run, but on closer inspection it appears to be just wiggling legs (near and far leg also are not differentiated).  If this is just a problem with my browser's GIF animation limitations, then please disregard!