Conclusion

If you are building a fairly complex mobile application, you should use Sencha Touch. jQueryMobile is good for smaller, less complex Ajax applications. Although jQueryMobile can be used for more complex applications, you will have to do DOM manipulation all by yourself and things will get more complex there.

Sencha Touch has a good performance and rich widget set. Some of its widgets use a data store to talk to the server components. You can use mvc design pattern with Sencha Touch and even split up your application into several .js files for improved modular code.