I've got a cake that I'm doing an airplane theme with. The cake itself is covered in chocolate ganache. I would like to make at least the top tier look like a sky with clouds. Would it be strange to frost the ganache with a thin layer of blue frosting? I'm not sure what else I could do.

I don't ever use ganache but I'm pretty sure lots of people use fondant on top of ganache. That's probably what I would do.

what about doing a white choc. ganache and color it blue?

Why don't you use a white fondant border that sort of looks wavy like clouds. The white would look nice with the ganache . I used that Wilton border cutter for this cake (I had fondant trouble, so please ignore the poor job, but you get the idea...) You could also use a cloud cookie cutter.