The principle difference is how the protocols communicate over the network. RTMFP is based on User Datagram Protocol (UDP), whereas RTMP is based on Transmission Control Protocol (TCP). UDP‐based protocols have some specific advantages over TCP‐based protocols when delivering livestreaming media, such as decreased latency and overhead, and greater tolerance for dropped/missing packets, at the cost of decreased reliability. Unlike RTMP, RTMFP also supports sending data directly from one Adobe Flash Player to another, without going through a server. A server‐side connection will always be required to establish the initial connection between the end‐users and can be used to provide server‐side data execution or gateways into other systems. The user of a Flash Media Server will also be required to authorize network address lookup and NAT traversalservices for the clients to prevent Flash Player from being used in an unmanaged way.
From wikipedia. RTMFP seems like the logical path for a new application. As for the usage of RTMFP/RTMP outside of Flash, I don't know.