Its unfortunate that this project is being deprecated but at least it came at the perfect time. I was already considering decoupling from WiringPi but was still planning on using it under the hood for low level I/O access from the C native library.
However, it's time to look at alternatives. I'm considering using pigpio project. This project also supports a remote interface via pipe and sockets. This could be a nice solution for the remote Pi4J features I want to support in V2.0.
I have started moving forward with the PIGPIO library. It allows for a direct shared C lib, pipes and socket integration. So this seems to be a nice solution to gain the remote I/O access that I wanted to support in Pi4J 2.0 without having to re-invent the wheel.
I'm starting with the socket integration as it should allow for faster development and testing cycles. It of course will be slower than a direct native integration, but we can add that once Pi4J 2.0 is up and working.