This question comes up every now and then but you have to consider the group of people who will be coming to this website. Most people who have a j-pouch and live out their lives merrily, won't be coming here.
As for me, I got my j-pouch in 1995 and have had chronic refractory pouchitis pretty much the whole way. When it is at its worse, I take flagyl and cipro and I find the side effects for both of those drugs to be considerable. So, I take them for 15 days each and then go off them until the pouchitis becomes unbearable again; usually about three months in between rounds. I've tried other anti-biotics but they either don't work or don't work well.