Things that I think would make Paint.net better:
1. the ability to right click while dragging to cancel the current action (or left clicking if you are drawing with the secondary color)
2. Eraser has independent brush width.
3. The ability to make new layers on the bottom of the stack as well as the top
4. A export current layer option (saves only the selected layer)
5. When selecting an area, the ability to hold down a key to switch to move selected pixels immediately after selecting.
All that being said, it is still a wondeful program.