Interesting mechanic, but I don't know if the game played on it enough. I felt like most points where I needed a specific color I just ended up waiting for the one I needed. I don't know if waiting is the best way to use the color change mechanic unless there were potentially some timed challenges where you needed to do certain parts of it before you switched.
Or maybe some of the flies could be different colors and after you collect them you could "spend" a fly to change your frog's color.
It is an interesting idea though that I think has potential in it.