Does WebViewer depend directly on jQuery UI? It seems like there are certain jQuery UI CSS classes in the minified CoreControls.js. If possible I would like to use bootstrap instead as that's what the rest of my project uses.
WebViewer uses many jQuery UI components but could be modified to use something else. If you wanted to switch to something else like the bootstrap UI then you would have to modify ReaderControl.html and ReaderControl.js which is unobfuscated. You'll see calls to .button(...) or .slider(...) for example that would have to be changed.
I believe that the jQuery UI classes inside CoreControls.js have to do with the sticky note annotation and a class for the selection rectangle. If you don't want to include the jQuery UI CSS then you could easily define those classes yourself. The sticky note annotation could also be modified yourself by hooking into the AnnotationPopupCreatedCallback