X-wing and Tie fighter were more easy to update, since the xwing vs tie fighter engine is nothing more then an enhanced version of the original xwing engine and later the tie fighter engine(xwing and TIE fighter both had another upgrade in a previous installment and re-released as "deluxe CD-rom" versions), they simply update the engine and re-release it(bit of a money maker, you are just paying full
product price for a (for them) relatively simple upgrade)
Wing commander 1&2, 3&4 and prophecy&SO use different engines, making the
best look of current technology(wing commander 1 and 2 looked superior to x-wing,
wing commander 3 outclassed tie-fighter, etc.
wing commander would have to start from scratch, sure the original designs would
be somewhere on the EA shelves , but you would need a completely new game engine, voice actors or even FMV actors, it would be a lot more expensive.