Cross-compatibility will be an issue if I do go native.
But what I would really like to know is how the Smoothness in Sencha Touch is compared to lets say Phone gap and other frameworks like them.
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First of all: Phone Gap is a native wrapper for applications written in a mobile
Framework like Jquery Mobile or Sencha Touch. That’s why you cannot compare them – they have different functionality. Second, there are plenty of different Frameworks out there but most people go with JqueryMobile or Sencha Touch. Look here or here for comparisons.
But to answer your subjective question with my subjective answer:
If you are planning a “presentational” application, which has some “easy” page transitions like fade or slide or Jquery hide and show stuff, you could use any of these two mentioned frameworks. They will be “smooth”. Just look at some examples.
If you are planning an “interactional” application, which has a lot of “graphical calculation” like a jump and run game, “image processing” or any “complicated”, respectively “fast progessions” of touch events, than stick to native. Your mobile web application won’t be “smooth”. Even though “light games” like Chess or Soduko are no problem with any of those frameworks.
Hope that helps. What I would do if I was in your situation: find out the technical bottleneck of your application. Take that performance critical functionality and put together a prototype in Sencha to get an idea. Check if your prototype is “smooth” enough. Don’t forget to check also more low end devices, as they have less processing power!