We have used both and we like Bootstrap for its simplicity and the pace at which it's being developed and enhanced. The problem with jQuery UI is that it's moving at a snail's pace. It's taking years to roll out common features like Menubar, Tree control and DataGrid which are in planning/development stage for ever. We waited waited waited and finally given up and used other libraries like ExtJS for our product http://dblite.com.
Bootstrap has come up with quite a comprehensive set of features in a very short period of time and I am sure it will outpace jQuery UI pretty soon.
So I see no point in using something that will eventually be outdated...
