Granted, Flash and SFM can look very nice when being done by the right hands, but there's lots of animation software that would create even greater results, both 2d and 3d. Here's a number of programs that fanimators could use.
2d: Toon Boom Harmony, Moho, TVPaint, Retas, Opentoonz
3d: Maya, 3DS Max, Cinema 4d, Blender
Duo Cartoonist is probably the only real example of someone in the fanimation community using such software. I wish the see more people do the same.