Mostly the animated transitions. I get about 4 frames total for the entire transition. Scrolling is also a little slow for the first few seconds after loading a page, but it quickly reaches normal speed.

I'm not working on any mobile webapp projects right now, but if/when I do I'll be sure to provide more detailed feedback on the issue tracker (if I encounter issues at that time), and otherwise contribute back to the community.

At any rate, keep up the great work! I finally took a detailed look at jQuery UI as a result of seeing this post and there's a very good chance I'll be using it in the semi-near future.