PSD Import/Export would benefit users that uses an IOS on the move but Windows at workplace. It also helps retain the layer and timeline settings if possible.

I'd love guides that could sit between pixels, and would be invisible on export. (Like photoshop or illustrator guides.) One could use them to set centerlines or easily align layers for an animation.

When making a large repetitive image I'm finding myself hitting copy/paste/merge-below multiple times. It would be easier if i could select part of the screen and hold down(a key or brush) to duplicate the graphic following the cursor. Almost like creating an instant pattern.

Being able to form a gradient fill with the ability to set gradient angle and start/end point would be great.

the result of pixen work can be one of:
-single image
-single animation
-character animation spritesheet

i think the least one needs a bit of rethinking.
it would be nice to pack few animations into a spritesheet of fixed dimensions (usually power of 2... 128x128 256x256...) and have the frames grouped by animation.
I like how this has been done in sprite something for iOS
http://www.youtube.com/watch?v=4_ZBI7KSI0M&feature=relmfu
basically you work on a big png and see a portion of it (the frame) then you makes animation by chosing sprites from the big sprite sheet.

Can you please add a "Library" section like Adobe Flash CS6 so we can add certain pictures to the current image/animation

the only major feature that I see missing from this software is a tool for dithering. Please add one!