One is discoverability. It's tough to find a bunch of scattered systems all over the place. That's a problem Facebook, Reddit, and HN address.
Another is identity. Tracking who's doing what (and what their permissions/authorities are) over a bunch of sites is ... a pain. I'm still mulling over a comment a few days back on HN that a user had 770 different password-based identities in their accounts-management storage (personal).
Search (related to the first) is a third -- spiders suck a lot of bandwidth. Unless there's some way to distribute search or allow nodes to self-report search elements (which will probably require some form of auditing).
And there's administration. It's really easy create systems any idiot can use, but then, any idiot will, and DDoS Brian Krebs and Dyn. Bulletproof administration is a real pain point.
There is merit in doing the technical work to make a decentralized paradigm easier, but the lack of an economic model is the tougher of the two problems.