LOVELY game idea. Trying to control two characters with such different abilities makes the experience much more interesting. Sometimes I found myself trying to move both at the same time just for the efficiency, or using the fly to make the ant path easier. That's really cool.
That said, I'd say playing as the fly is much more fun. The ant slow movement affects the game pacing, and it can be painful to complete a level when one of the characters dies and you have to repeat everything again.