It would be a nice immersion feature to have skins either a) selectable when joining a mission (preferred), b) selectable by the mission creator, or c) have the last skin selected for the aircraft that happens to be used in the mission remembered from the hangar.
The mission tool is a really neat function used by a few squads in the FSO. It would be cool if we could further distinguish squads in like aircraft. Yeah, yeah we have colored icons... this is more of an ego/screenshot reason.