if you are really into getting a joystick to work, you can use Xpadder. a controller-mouse/keyboard emulator that works awesome. takes some configuring but works better than you would think
Frontier had much of what you describe back in 1993. Pioneer is a modern remake that I'm involved with. We do have a little bit of handwaving because ultimately we're making a game, but we think long and hard about the balance between realism and fun, and I think we're doing pretty good.
Its still early days, but we're putting flesh on the bones. Nerds welcome!
I will give it a shot in Linux when I have the time and post the results here :) Wine behaves a little differently on Mac than on Linux. If I remember correctly with Wine Tricks and Wine Bottler you can make windows exe into Mac DMG and mount the images and run them natively. Not sure how it will work with Rodina. Unfortunately my Mac does not run OS x any longer. It is only running Linux. so I can''t test wine bottler out with Rodina. I have had other windows games running on Mac with Wine Bottler though.