I'm pretty sure that if the controls can't be switched around, they would make it favourable to right-handed pilots - so the throttle would be on the left and stick on the right.
Other than that: Consider removing the pilot model from the internal cockpit model altogether, and only have it rendered on external view. Having legs and arms in the cockpit often surprisingly decreases immersion, which is the reason most modern flight sims don't have pilots in the cockpits. It also removes a lot of clipping issues.
Placing view point on slightly higher position should help with cockpit visibility forward. How is the visibility backward? Most ships insist on putting a massive bulkhead (or worse, massively wide headrest of the seat) right before pilot's head, restricting visibility with no reason... most ships in FreeSpace have simply horrible (read: nonexistent) rear/shoulder visibility which is one of my pet peeves in the series - there is zero reason for not making the cockpits have reasonable visibility in designs such as Apollo, Valkyrie, or Perseus.
I would love to see a cockpit design with similar layout as modern fast jets - bubble canopy, blended to the fuselage, no massive struts, and free view over shoulders, around the ejection seat's head rest. That's what would make the most sense in a FreeSpace 2 ship, especially after they came up with shields...