If going to Kyoto, I'd say that taking the Shinkansen from Tokyo or Shinagawa is generally preferable to flying into Osaka, and gives you much more flexibility if there is a delay or change of plans since there is a train literally every few minutes. Keep in mind that you can ship large luggage from the airport to your hotel in Kyoto for like $20-25 a piece, so you don't necessarily need to carry it onto the train.