I manage my ebooks and ebook library loans exclusively with MC. I use epub, pdf, doc, txt and rtf. I have no experience with mobi.
I find that MC is a vastly better manager than what I understand is the "premiere" dedicated ebook manager, Calibre. I call the Calibre reader as a double-click file association within MC, as well as the Adobe PDF reader. Stripping the file management away from both of these programs makes their use tolerable, barely. I would love to read and tag ebooks using MC only, but the last time this topic came up there were maybe three people showing interest, so I would not expect JRiver to pull programmers off their current priorities for this.
If you have a large library, do some fooling around with custom smartlists, and you'll really see the power of MC. I have attention span issues, so there's probably 5,000 books I'm halfway through. Smartlists make it easy to keep track of these things and reassure myself that one day I could finish something, if I cared to.
I know that JRiver will increase support as the demand increases, but in the mean time they'll appreciate specific feedback from early adopters.