I'd prefer to stay in Kyoto because on a first visit I'd probably find more to interest me in Kyoto. There are always some people like to say that "Osaka has the food and the nightlife".... Yawn. I think they're mostly people who found Osaka more affordable than Kyoto (it usually is) and don't like to think that Kyoto might have had food and things to do at night (it does).

Based on what you've said about points and prices, I'd suggest staying at the Ritz Carlton in Tokyo and the Hyatt Regency in Kyoto. Both fine hotels in great locations.