Conclusion
I would not recommend combining JQuery Mobile and Bootstrap for complex projects.
JQM Knowledge
We are building a series of sophisticated web application all using the JQuery Mobile (JQM) Framework. We have spent over a year producing this and now have pretty reasonable knowledge of JQM.
Positives: Some of the features are useful such as persistent footers and the mobile friendly components which give the HTML5 app a pretty native feel.
Negatives: We have had to disable quite a lot of features of JQM such as preloading pages to create the complex functionality we required.
The end result is good as we have fooled iOS developers into thinking it was native.
Bootstrap Knowledge
I have also recently produced a responsive website using bootstrap to advertise the above JQM product and that has worked out very well (http://www.sure-sense.com).
The Combo
I tried to combine the bootstrap with the JQM project on a dashboard application but that has quickly highlighted that the 2 frameworks are not compatible. The CSS of JQM marks up the components on top of the bootstrap CSS and the results are some components looking like JQM and others like bootstrap.
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