Beside many of the already mentioned requests I would really like to see more detailed options for the weather effects. Although, the current system of normal, overcast, rainy, storm is easy to access for beginners, it makes it very difficult to "simulate" a weather change mid-session. A more gradual approach with sliders like in the normal 2D-Editor would be much nicer!
Futhermore, more options for the awesome fog would be great, for example a density slider! :D