Sapporo to Kyoto

If you left on the earliest possible train around 6:30 AM you could arrive in Kyoto at 7:11 PM, killing about 12 hours and 45 minutes. You'd certainly get your money's worth, but you'd pretty much lose the whole day sitting on trains. Alternatively, you could fly using a low cost carrier like Jet Star or Peach, fly for as low as ¥4,690 in just over 2 hours, and still have the whole day for sightseeing. Which do you prefer?