We are using NGUI to draw an isometric view of a city. The whole city, including static & dynamic sprites, is being drawn with NGUI. Yes, we know this isn't what NGUI was designed for, but it does handle it extremely well
The only problem we have right now it that we have some gameplay graphical elements that are the same across all levels of the game and some other graphical elements that change from level to level (building for different cities). So we would like to have one atlas for the shared gameplay elements and one extra atlas for each level of the game. Right now we can't do that because we need some of the gameplay elements (mostly vehicles) to be drawn sometimes behind a building and sometimes in front of it. Our code dynamically changes the depth of the gameplay element to handle that, but it only works if all the sprites come from the same atlas.
Unity can handle multiple materials on a single mesh, so I guess it might be possible to have NGUI put all the widgets from a single panel into a single mesh even if they use different atlases. This would solve a huge problem for us, because right now each atlas is twice as large as it should be due to having to place a copy of all the gameplay elements in each level atlas. It is a web based game and we need to reduce the download size as much as possible.