Wtf use an actual art program for coloring scanned drawings :troll
Also
-The "messy overdesigned multi window interface" isn't too much of a problem, you can close all the windows except for the color and tool windows... and the color wheel isn't too complex to understand either, it's pretty...
Paintdotnet clears ms paint for pixel art i am SORRY
However, if you don't want to use it for whatever reason you could try Libresprite, or compile Aseprite yourself if you don't want to buy it