I've been using Pyxel Edit for several months now and I can say I'm absolutely in love this program. I think I'm using it for 80% of my pixel works.
The thing I don't like is the color window. I'm really used to Photoshop sliders, and still don't like Pyxel ones. Also I heard that a color wheel is a good practice for artists.
Also when using a separate window means I lose focus of main drawing window. For example when I tweak sliders and then press B to switch to pen, then the color window registers this press, not the main window. This gives me the most "Damn it!" cases with the program. Could we have a color tab on the side column please? Maybe somewhere near palette.
Edit: forgot to mention color window always covers much of the interface or working space, leaving less space for work.