I get a lot of questions about how I did page routing and page transitions when I transitioned. I ended up writing just a few lines of JQM-inspired page changing code - since it's a PhoneGap app, I didn't need to worry about changing the URL properly - just changing DIV visibility and some event triggering. When I was using jQM, I had disabled transitions, so I didn't go through any effort in re-implementing those in Bootstrap.

But, yeah, if you're really keen on that stuff, then my choice may not be the one for you.