I'm nearly finished developing the desktop version of my game, and the plan is to do the mobile version next. Because it has a lot of large graphics and many entities on screen at once, I need to use one of the accelerated canvas options, so we're looking at appMobi or CoccoonJS. We have a ton of UI (game over, account stuff, upgrade purchasing etc.) done in HTML. Should I try to get a solution working that uses a UIWebView type hybrid solution, or attempt to move everything into the game engine?

I should mention that it actually works pretty well doing the hybrid on the desktop. I use jQuery to dispatch events on the document object from within the game engine, and listen to and respond to those events in the game's host page. This lets my designer work with the HTML/CSS he's familiar with while I concentrate on the game mechanics and logic.