WhatsApp's popularity originally came from how it ran on many WAP phone systems, not just iOS and Android but also all the feature phones. What they did looked crazy from the outside but they effectively re-implemented SMS at a lower cost, for nearly all phones. That was not a trivial amount of effort, but it produced a lower financial friction than competition.

A disrupter would have to have even less friction but would be competing against a product that already has a significant network effect and a very generous backing by Facebook. I'm speculating that FB will eventually nudge WhatsApp users to Messenger, or find a way to gradually merge the services to the point where they are identical, especially w.r.t. advertisement.

In that respect, it was brilliant of FB to acquire WhatsApp: not just for the users, but to make it hard for any newcommer to disrupt things (hard to compete againsts free and frictionless).

WhatsApp was originally XMPP, and may still be some hacked up version of it.

There are many (open-source) solutions for building your own secure messaging system, XMPP and others.

I'm happily running (I should also disclose: developing) my own server and talking with friends and family who use e.g. Conversations as an alternative to WhatsApp.