I'm no mod but if I were to create a paint program just for pixeling it would only need a few tools, most important of all being a easy to use palette:
1. Palette ( ability to load up colors, save palettes and maybe some hotkey mechanism to switch colors )
2. Pencil ( just like mspaint, left click paints, right click paints, if I click my palette it grabs that color )
3. Eraser ( instead of an eraser, I think it would be more beneficial to have a transparency color in the palette tool, use that to erase to trans )
4. Layers ( Only need 2 layers for any kind of pixel art, to easily move stuff around or to save an old copy of something for comparison )
5. Select/move tool ( a select tool you can use lasso with right click, square with left click, use shift for uniformity )
6. I also think a hotkey/button to select whatever color your cursor is over while using the pencil tool would be better than an eye dropper.
Honestly, there are tons of programs to pixel with, the benefit of creating something new would be for speed and efficiency using the tools. Its better to expand upon something that was already created, than to create something new that already exists.
my 2c
later.