MAVLink v1.0 will be released soon, bringing a number of new features and a substantially cleaned up protocol to the community. It is however still under review, so adopting MAVLink now would thus offer you the opportunity to shape the protocol.
It would be great to have Paparazzi and QGroundControl working together and I'm willing to help in the integration and adjust QGC where needed.
I've substantially improved QGroundControl over the last few weeks, the most notable differences are some cleanups in the user interface and a factor of 2x-4x in speedup - it should consume substantially less CPU now.
Here is a video of the latest features, including some customization that would allow you to tune controllers.
It should be rather straightforward to port MAVLink to Paparazzi. Of course it would need some effort, but it shouldn't involve difficult steps. I would be ready to help this process by active help on this mailing list and changes to QGroundControl where needed.
For testing the current version, I recommend to build from source, it is quickly set up, or to download the v10release binaries from the downloads section of the website.
If you're on Mac OS or Windows and don't have a build environment installed, you can download QGroundControl v1.0.0 here. PLEASE NOTE THAT THESE ARE ALPHA BINARIES! They are well tested and did not crash during the tests, but do not reflect at all the final application stability.
A few more links with useful information:
How to add MAVLink support to your autopilot:
The new mission lib (makes parameter and waypoint support a lot easier, see the testing folder / main.c for a working Linux example):
Available ground control stations for MAVLink: