Stipulate that Tor's encryption is modernized and drastically improved. I still don't think it's a good idea to build a messaging application directly on top of that, for some of the same reasons that it isn't a good idea to simply run a messaging application on top of TLS or Nacl. The service model and security requirements for a simple transport are different from those of a messenger.

That's what's so exciting about the WhatsApp announcement. WhatsApp is by all accounts a pretty great messaging application, and it doesn't just have decent encryption now; it has best in class encryption specifically designed to protect a messaging application, designed by experts who thought about this problem for a long time.