As for transitions to complex pages, it gets worse. So bad for us, in fact that we had to turn the transitions off entirely. Obviously something we'd like to remedy.
Our situation is probably one of the most complex use cases, but something that is quite common in the mobile arena. We are using Bing maps to plot locations, and we have overlaid icons and jQM controls in DIVs over the map. (This is a method Bing Maps 7 recommends, BTW. We're not doing anything unexpected here.)
When a transition occurs (all it is is a basic slide transition) the controls display for about 1/2 a second and then disappear. But not always. Sometimes the page shows with the controls hidden and then they suddenly appear again. We spent ages trying to understand what was causing this, until one day in frustration I just set the default transition property to 'none'.
And voila, no more disappearing controls.
(This is on an iPhone with PhoneGap.)
My suspicion is that the transition is somehow taking an 'image' the screen it is transitioning to, doing the transition and then triggering a redraw of the screen when the transition is complete. However, it seems that complex pages may take longer to redraw than the transition is allowing for, or something like that.
I would love to see a resolution to this. Meanwhile, our app will not be able to take advantage of the slick jQM transitions at all. :(