It's not cheap, but the
WCP Spartan Board is a great solution (IMHO) for the RoboRIO connectors. It offers a variety of nice features, but one of the best is that it changes all pinouts to Molex connectors with detents. We used it this season and never had any issues with wires coming lose on the RIO. It doesn't solve the PITA crimp problem, but it's an improvement.
I know you guys work closely with some super sweet 3D printing, I've seen a handful of solutions floating around of 3D printed attachments which help retain PWMs in the RIO. I don't have a link to any but I'm sure someone will post one. I seem to recall 111 Wildstang put a version for download up somwhere.
As for pneumatics, I've always used the push-to-connect fittings so I can't recommend any alternatives, but I can say that it matters a LOT if the tubes are cut flush 90*. This is the most frequent failure case for the push to connect fittings as far as leaks or staying engaged. If there's any angle at all on the end of the tubes they won't seal properly which can lead to them coming out.