The unused part of the stomach still produces acid and stuff to help digest food. It reconnects down lower in your intestines to help digest the food that goes through your pouch. And like others said, it still produces hormones, though I'm not sure that's the main reason it's left. I think it's there to improve digestion, since your pouch alone doesn't make enough acid to do the job. That's the way my surgeon explained it, at least.
