Are the older Wing Commander games flightstick only through the missions at all?

I would love to answer this question, but I'm afraid I don't understand it. I'll get it a shot anyways: You can play the whole game with just a joystick, but it's more conveniant to use a mouse when you're not in the cockpit. But you can do it. Well, I take that back partly. You can certainly play it without using keyboard shortcuts, but it might be a lot harder. I used to use the Thrustmaster F-16 stick and throttle which provided enough button combinations to do everything without the keyboard. Depending on what flight stick you use, you might want to use something like xpadder.com to get some keyboard emulation through your stick.

Another point: WC was closer to "simulation" than "arcade", so to play it properly, you need a lot of buttons. Whether those are on your flightstick/throttle or on the keyboard... you need a lot of buttons.

WC 1-3 added support for throttles in the WC Trilogy release or whatever it was called. I think 4 and onward supported throttles (both digital and analogue) but I'm having a hard time remembering exactly. My only point is that you might want to look up the Windows95 re-release of 1-3 as they did add some features. And make sure you look up Privateer 1. It was the best, and probably the one that survived the best. wcnews.com is a good resource for the modern Wing Commander fan.