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Nice use of Photoshop, Illustrator, and Flash!
I like using these three programs in conjunction, too.
One tip: Reduce the size of the final animation by vectorizing some of your raster images. It's not a good habit to get into when your animation comprises lots of raster images, which would lose no quality as vector drawings. It's better to reserve raster artwork for special effects, such as smoke, fire, or other related atmospheric effects, not as main characters.
You should have converted to vector format...
Flash has an auto trace feature. Or, the original vector drawings should have remained in Flash, and Photoshop/After Effects visuals should have been imported as bitmaps (PNGs, to be precise).
It's nice to see you've entered the realm of 3d!
A hint for next time: Use Flash's autotrace function to vectorize each frame of the animation. You'd remain within size constraints, and besides, arificially "vectorized" 3 dimensional Flash animations are neat.
Amazing!
This is quite possibly the most faithful flash-based video game simulation I've ever seen. If this were a standalone game, I would have thought Capcom and Nintendo in a rare joint venture created an obscure title for the NES that I had not yet discovered!
This feels like the real thing! Now, you must make a MegaMan X vs. Samus (Super Metroid Version).
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VisionTribe Hangman 
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Megaman vs Metroid 