I guess that depends on if there's anything else you want to try and do that day. Universal would probably fill your day, but Warner Bros. would allow you to do other things too, so that's up to you. One other piece worth considering: do you have any interest or plans in attending Universal in Florida any time soon? If so, I would skip Universal in California. Florida has more Harry Potter offerings and is better overall IMO. The Studio Tour is pretty much the only thing that Universal Hollywood has that Florida does not. If you're going to Florida anytime soon, pick Warner Bros for sure.
Another question to think about: Would you rather (probably) see some of the actual props or costumes used in the movies, or feel like you're living in them? That might also sway your decision.