I think the tooling will improve significantly this year and you should see people able to build protocols with zkSNARKs soon -- without spending days figuring out how everything works.
I'm building something in Rust called bellman (https://github.com/ebfull/bellman) which should make it easier to construct circuits safely and build these proofs easier, but it's in its early stages.
These are some interesting reflections on the present state of the tech by Gregory Maxwell:
https://www.reddit.com/r/Bitcoin/comments/47rk85/first_succe...
I suspect there's a great opportunity here for startups. The theory is sound, and tooling (UX) needs to be built around it.