End to end encryption is probably one of the last big things we've yet to fully tackle, unfortunately. Though hopefully we'll fully begin to start spec'ing that sometime soon!

One of the major things we want is the ability for e2e encrypted messages to still be readable from all of your devices, which is kind of incompatible with OTR. Saying that, people have been talking about building OTR on top of Matrx; either by embedding OTR messages directly in the message JSON or using Matrix to negotiate a data channel with something like webrtc.