Flagyl alone never worked for me, and Cipro worked like magic, so it’s possible that effectiveness will drive your choice. In terms of side effects Flagyl probably has the edge. Cipro carries a “Black Box” warning from the FDA about tendinitis and tendon rupture, meaning (basically) that you shouldn’t use it if there’s a good alternative available. Some people do find Flagyl intolerable, though, mainly because of the metallic taste.
I’ve been using both continuously for years, without problems.