I agree with everybody who has said - do what you like. Be creative.
After seeing a Mustang and a Spitfire at a local airshow I had an idea of how I want to display the P-51 that I have on the dock. The sight of those baby's screaming along at low altitude with their gear being pulled up while they are still so close to the ground was one of the coolest sights that I remember from the show. I'm planning on doing the P-51 with a clear plastic disk to replace the prop blades, and the gear halfway up.
Most of my kits are displayed with gear down and a pilot in place - either suspended or sitting on a shelf. In fact, the only "gear up" plane is a Spitfire that lost a battle with my five year old. If it ever comes down - it will have to be a belly landing !
For myself - I really prefer to have the pilots in the plane, but if the canopy is open I don't glue them in. Another thing I do is chop their heads off... and then glue them back on, turned to the side. I think they look kinda robotic if they're just staring straight ahead. I've also chopped off arms and legs and re-positioned them so that they appear to be waving or entering or exiting the cockpit. I just think it lends a little personality to the whole model - kinda like capturing a moment in time.
I was a little miffed, in fact, with the last two 1/72 scale Hasegawa kits that I bought because they didn't include any pilot/crew figures at all.