The Shinkansen has to be the best choice, surely?
It would definitely be the quickest and easiest way.

Flying would take longer, as you'd have to fly to Osaka airport and then take a bus or train to Kyoto. It would also be much less convenient (having to transfer) and probably be more expensive in total.

I've never been on a long-distance bus in Japan, so maybe my comment isn't fair. But.. they can be hellish. They tend to be less comfortable than by train. I've been on 'executive' long distance buses with 2-1 seating and probably 50-60 inches of leg room with seat that go to an angled lie-flat. It was really bad and I regretted it and would gladly pay triple to fly it if I did it again. I can only imagine with narrow Japanese-sized seats it would be much worse.
You also always have that feeling less than half way there that you would already be there by train or plane.