I tried both.
AN is a must have for me because of the immersive interiors features.
AN also add hundreds of new weathers.
Atmospheres adds only a few (20 max)
AN allows with the ini file a little more customization (duration, fog, colors, night brightness ...)
I use AN for the interiors, and Atmospheres for the weathers. Because I like the new textures and the weather colors. I also prefer to have a few but perfectly tweaked weathers than hundreds of weather with half I don't like.
The best is to try both and test the weathers with this mod :
http://www.nexusmods.com/oblivion/mods/46247/?
Some weeks ago I made 2 screenshots to compare (morning, clear weather) :
http://www.nexusmods.com/oblivion/images/163101/?
Maybe it can help you decide (or not )