I had already explored the possibilty to add an epub reader in Ubooquity, but at the time none of the libraries I had tried (Monocle and Readk.it were working correctly).
I did not know epub.js. I'll test it and consider using it in the future. Thanks for the info !

I'll add it to my todo list.
(this sorting criterion is already available for comics ("Sort by path") but not for ebooks indeed)

You can do that with Ubooquity 1.6.0 (released yestarday).You have to configure Ubooquity to use a port different from 80, then choose a reverse proxy prefix and redirect traffic corresponding to this prefix and the port you have chosen to Ubooquity.

For instance, if your server name is "myserver.com", configure Ubooquity to use port 2202, set the reverse proxy prefix to "ubooquity" and configure your IIS/Apache/Tomcat to redirect all traffic corresponding to "myserver.com/ubooquity" to "localhost:2202". (prefix and port number are only examples, use what you want).