PE is really helping me with my animation job, so, first of all, thanks! There's a few things I'd suggest (some of them are related to how photoshop works, since that's where I used to do my pixel-art work) that would help improve the workflow.
1) Transform seems a bit wonky right now due to the fact that you need to select first before transforming (which complicates things a bit if you're looking to transform the whole thing). Is it possible to make it select the tile/layer by default without having to make a selection?
2) The selection outline doesn't appear in the frame edit view, which is a bit annoying since it's often used in animation.
3) Is it possible to give another crosshair option like the pixel "crosshair" (that little square outline that changes size as you increase the brush size) in photoshop? it feels more intuitive for positioning pixels.
4) Opacity option for Bucket tool and blend modes for strokes/fills.
5) History window would be a cool, minor addition.
6) (This is the most far-fetched) Indexing your palette option. It would be really interesting to limit your palette like how Graphics Gale or
PS's HD Index trick works.
7) Like some people've said, dithering patterns would be a time saver.
Also, I'm not sure if I'm using it right, but the dotted line option doesn't seem to work properly. doing a free stroke doesn't change anything, and making a straight line simply creates 2 pixels, one at the beggining and one at the end.
Cheers!