9-patch kills performance - it's not nearly as resource-friendly as tiled backgrounds.
When importing art, test as you go. No point in dumping in everything in one go and then testing. Graphics are the biggest performance killer in C2.
I spent a lot of time optimising my artwork as I got it in from the artist. You can't simply drop in whatever comes through and expect everything to be smooth. Battlefield 3 was built by a team of skilled engineers and artists who work to spec, and the art pipeline is one of the most complex parts of any AAA development program.
The quality of the PNG won't make any difference at run-time, it only affects file size, but as soon as you have multiple transparent and semi-transparent images all on top of each other and/or moving around, you can expect performance to suffer.