You can run RS over Tor. In fact, IIRC RS is in Whonix.
That's one way to screw with the "no filesharing" ban in Tor, which has positive and negative consequences. I do like the idea of layering a network of pseudonymous trust over the Tor layer of mutual distrust, but is that not horrendously slow?
RS could have profited from a less is more approach. E.g. running NNTP could have allowed you to use standard clients. In general I'd much prefer to connect with known (SMTP, IMAP) protocols to localhost rather than poking an unstable, monolithic blob with usability from hell.
This sounds like i2p; a P2P networking layer for applications that need not be routing-aware? Although again; i2p creates a system of mutual distrust whereas Retroshare assumes mutual trust. The advantages and disadvantages of either depend on entirely social factors that are hard to model (see [Cryptography][Law] thread on range of estimates regarding rat-content of hacker community), so as far as the philosophy I'm not prepared to call. Certainly it's easier to establish a route using Tor/i2p than with Retroshare, and it's doubtful you could have true anonymity if your friends can see when you're online and correlate with activities of public identities they may notice through shared interests. But then, that's not what Retroshare is for; it's for creating networks for social and personal use.