One thing you can do in MS Paint is colour replacing. Here's how to do it in Ms Paint:
Select the colour you want to change as your primary colour.
Select the colour you want to change it TO as your secondary colour.
Using the eraser, right click and move the cursor over the image.
Bam. It only changes the colour you selected and changes it to the other colour you selected. (if it doesnt work, cut and paste the entire image then try again)
Functionality similar to this across the whole image or as a brush would be fantastic, as it is incredibly useful (especially if it isn't buggy like MS Paint because that can get quite annoying).
Looking forward to more features as its developed!