I don't use jqmobile-patch.js. I haven't used it in some time, even with JQM 1.3 and 1.2.
It contains MOSTLY support for wait pages, which I do not use, and which I think is an extraordinarily bad idea anyway.
You will have to look if it has anything else that you need. There is some stuff for WP7 and BB6 and Android 2.2 as well.
I also do not use any of the CSS in public/css. All of this would not work with JQM 1.4.x. And it's quite dated in terms of design. The standard JQM look is much better.
You will have a big job updating if you already have a big project! It's made somewhat easier because deprecated does not mean removed, and some of the removal has been pushed forward from JQM 1.5 to JQM 1.6. Even so, you will have to make a lot of changes.
There is a transition guide that is quite helpful: