a better "swarming" file transfer protocol could be written. with the right features it could become enormously popular almost overnight. i think bittorrent's tracker is a big weakness. i love the TCP/IP / ethernet specific tweaks that cohen put in.
if i have even pieces of a file, i should be able to trade with other people even if the tracker is down. there should be no single tracker. we're all trackers. any one of our IPs can be the entry point into the swarm and any member can go away. Thats almost true for bittorrent, except for the tracker.
other features would be to re-address the whole idea of peer discovery, and to look at different sorts of sharing including searching and cataloging, and a streaming option - get the pieces in-order.