We're actually using hardware-accelerated CSS-based transitions based on jqtouch. The difference is that jqtouch doesn't scroll you back to the position you were on if you navigate back - you always scroll back to the top, then transition so if you're on a long page, click a link, then go back you lose you place. We think that remembering you position is a very important usability feature that's expected on the web so this is included in jQuery Mobile. Unfortunately, it introduces a blink or jump which makes things feel much less smooth.

Page transitions, especially on iOS are an incredibly important issues for the team and we're actively working on improving this. In fact, we have 3-4 different branches exploring various approaches: https://github.com/jquery/jquery-mobile/issues#issue/455

We weren't able to find a solution in time for a3, but this will continue to improve.