I've gotten this game running no problem on Windows and Ubuntu Linux, but found something odd on the latter. I can't get my plane to launch from the carrier in the first mission with throttle up from the controller, only with the space bar. Everything else seems solid so far.

Strange. I don't know what could be the cause. It's strange if the keyboard works still. Do  the other controller functions work normal? Can you control the throttle with a controller after taking off. Does your controller have analog input on the triggers? My best guess is that the game reads the analog input differently from the keyboard keys.

The controller works perfectly once takeoff is done. I'm not sure if the triggers are analog, I'm using an 8-Bit Do SNES+ Pro at the moment. 

Okay, thanks. That gives me somewhere to start looking.

Hey again, did some more playing around with an Xbox controller, same behavior on that version of the game. Still launches just fine with the space bar. Managed to play through the rest of the available missions on Ubuntu with zero issues. This glitch aside, game is fun as all get out and I'm eagerly awaiting the full release.