Hmmm. I'd agree with joniveson and stay in Kyoto. Unless 10,000 shops underground rock your boat, in which case, why not? But in Kyoto you could see temples, shrines, a mountain walk or two, pop down to Nara, and get a feel for a different side of Japan only a few miles out of town. Osaka is a "wannabe" destination: they want you to visit, but we don't want to go. An entire city of pigeon poop disguised as concrete.
For the international visitor, skip Kobe. It's more fun for foreign residents. Piss-poor waterfront, mediocre shopping. I know, I know, truth hurts. Stay in Kyoto, then rent a car for a couple of days (dirt cheap) or get the train. You've already discovered the train works.