I had some issues with the bottom analog triggers sticking underneath the top digital triggers. This made playing Pinball Arcade very frustrating. The solution was to file off the useless tabs that were sticking out of the digital buttons. I also widened the holes for the action buttons. The controller works beautifully now.
Hopefully the controller issues are fixed for the Tuesday Ouya release. There should be a lot of content coming over the next few days and weeks since many developers have decided to wait for the official launch to release software.
Photostream detailing the areas that I modded:
http://www.flickr.com/photos/30203515...