This idea may be similar to another already posted idea but this is what i like to see.

When creating a single image i like to be able to register a selection, give it a name and continue editing. After creating my sprites, registered them all and gave them a name i want to export all sprites from this single image to (PNG) files with the given names. for example: i created a helicopter, tree and a ball and named theses. After exporting the sprites i want these files on my disk:

helicopter.png
tree.png
ball.png

Now i can process them in my own selected sprite sheet tool.

After saving the pixen file i must be able to reopen the file and make changes and sprite the sprites again.

Removing a selection, changing width and height or rename it must also be present. Thanks ;-)

While editing a sprite, the frequency palette may miscount colors used, displaying incorrect results.

When changing a palette index's color, it may appear incorrect in the frequency palette, and cause miscounts.

The only way to refresh the frequency palette is switching between it and the recent colors widget.

When switching between the recent colors widget and the frequency palette, the frequency palette may display incorrect colors (typically after changing a palette index's color)

After double clicking on a palette index within the frequency palette, it is not easy to exit the palette editing mode. (E.g cannot "deselect" the palette index without switching to the recent colors widget)

The values in Apple's HSB Sliders color picker seem to be inaccurate; When I set the color using these sliders, then switch to another color and back, the values are not what I originally chose. (May be an artifact of the conversion to RGB)