I would be happy with full syncing an Apps/Marvin folder through the Dropbox Sync API. But I really only use my iPad for reading and I am happy to hand over 30-40GB of storage to Marvin. I can see that is probably not palatable to others.
I would also be happy with a daemon running on my computer that keeps track of the epub and extracts metadata and cover pages etc to a catalog file that Marvin would download. But again I can see that this is inelegant, synchronization will happen only in when the computer is running...
I would also be happy with a Calibre plugin that does the same thing.
Or to to keep track of epubs in dropbox without downloading to the iPad you could consider something like this:
Either to use it directly or implement something like that yourself. Though I am sure that it involves a heavy server-side component. I am sure they sync the dropbox to their servers to achieve this.