In terms of convenience of the routing, KIX is clearly superior. From KIX you take the limited express Haruka (not a bullet train) directly to Kyoto, takes about 80 minutes.

From NRT, you either have to fly to the Osaka area (either KIX or Itami airports) and then proceed as above, or you have to take a train to Tokyo followed by the bullet train to Kyoto.

Since air fares are commonly the same SFO-NRT and SFO-KIX, it's both faster and cheaper to go via KIX. Only you can decide whether the extra comfort of the flat bed seat is worth the additional cost and time.

Note if you want to use a confirmable upgrade, I've noticed that UA has currently clamped off virtually all confirmable upgrades on the SFO-NRT route, which used to be one of the easiest to upgrade on.

Check out the Japan forum, this topic has been extensively discussed recently there.