To me, Japan is all about food, hot springs, cool trains, shopping. I personally have no interest in temples or other old buildings. I'd be much happier staying an entire week in Tokyo or in Osaka and spending the week eating and shopping and maybe taking one side trip out to a nearby onsen. But that's just me.
So that's what you have to answer for yourself. Are you interested in sightseeing primarily? Or do you want to stay put in one city and then hang out and explore?
And if sightseeing is what you like and if that entails both Tokyo and Kyoto, then it's probably worth getting the Rail Pass.