I like cockpits only if they fit in with the game graphics. My first Wing Commander experience was WCIII. I remember how annoyed I was with the cockpit being up; I turned it off as quick as I could. I recall something had a white tint to it (probably the pilot legs and stick) that didn't match the outside. It interfered greatly with my field of vision and got in the way of feeling immersion because it looked unrealistic.
After I played WC1, I learned to really like the cockpits. The look of them as well as the different types and locations of the gagues really made you feel like you were in a different fighter. The odd setup of the Scimtar's especially gave it character. The inside of the cockpit didn't clash much with the colors, resolutions, and graphics of the outside. The cockpit had the opposite effect of Wing Commander 3 since it increased that feeling of immersion.
I voted for keeping cockpits on this, but only if they are done well; more like WC1 than WC3 (WCP was ok I guess, but I definitely prefer WC1).