BCS is a little bit better at making a distinction between pilot and mecha, as well as making repairs between missions a thing that players have to worry about. It also makes grunt suits much weaker though, so PCs on those have to fight weaker enemy formations (roughly 75% of the usual power rating) to make the fight winnable. YMMV on whether this is a good tradeoff or not.
Thanks for the support! Regardless of the system you use, best of luck with the game.