I'm sure others have suggested this, but here are my suggestions.
1 ) Allow for transparent, alpha-channel enabled PNG files.
2 ) Have a block to change sprite display speed (e.g. 1x, 2x, 0.5x, variable x). I assume there's already a method to do it in code, so that's not necessary.
3 ) Use pixel amounts instead of columns and rows for sprite creation. For example, when I wanted to create a sprite from a file, it asked me how many columns and rows I wanted - it'd be easier to just tell it to split it up into a 16x16 cell-size (20 columns, 15 rows for 320x240).
EDIT: Which the tileset editor already does.
4 ) If a cell in an animation is blank (wholly transparent), discard it. Also, add an option to add a blank image into the animation.
5 ) Allow for click and drag to move an animation about.
6 ) Allow for Undo and Redo for the sprite editor.
7 ) Set Copy and Paste to be Ctrl-C and Ctrl-V.
8 ) Tell me if I'm about to remove an animation, and have a 'Don't Remind Me Again' option.
9 ) Give a 'Don't Remind Me Again' option for sprite image removal. Being asked each time I'm trying to remove a blank frame can get annoying.
10 ) Give a zoom feature for the sprite editor when looking at a sprite sheet.
11 ) Allow for joystick input. Sometimes Keyboard and Mouse just aren't enough. Not sure if it's possible with Flash, but that would be a nice addition.
So... Those are mine. This is a pretty interesting piece of software. So far, I'm pretty impressed, particularly with the Forge idea.