Originally Posted by
ksandness
It depends on what your priorities are.
If cheapness is your priority, then a low-cost domestic flight or an overnight bus (ugh) may be your best options.
But the JR Pass will give you a ground-level view of the countryside and smaller cities between Tokyo and Kyoto, a quintessential Japanese experience (the Shinkansen trains), and the ability to take excursions out of either city at no extra charge. (BTW, the JR Pass is good only on JR trains, not on subways or private commuter lines, but JR will take you all kinds of places intercity.)
In my particular case, as a first-time visitor to Japan who isn't on a super-tight budget, I'd rather ride the train and see the countryside in comfort.
Side question: I notice that my points in various hotel chains don't seem useful in Kyoto, because I don't see any familiar chains there. Strange.