Well, for that stay, either Osaka or Kyoto would work. I'd recommend Kyoto for a one-and-only visit. Osaka has its charms but is more of a modern, big city. Kyoto has more of the temples and such.
The airport express train "Haruka" takes less than an hour to Shin-Osaka Station. You would take a subway or cab from there to get into the city. The same train goes on to Kyoto, taking 75 to 90 minutes depending on departure. The Kyoto arrival comes in to the main Kyoto Station.
From Kyoto Station, it is a short walk north on the main road from the north exit (Karasuma Exit) to Higashi-Honganji temple, one of the larger ones in the area. Just across the street from the temple is a nice Japanese garden. If you really want to get away from the station, take a cab to one of the closer sites like Sanjusangendo Hall, Nishi-Honganji temple or Yasaka Jinja (shrine) in the old Gion neighborhood. Just be sure to watch the time. For a more adventurous option, get on one of the tourist buses - #100 or #101 - and ride around the tourist loop.
At Kyoto Station, there are numerous places to eat, find a souvenir, take a picture (the roof - up the escalator) and arrange your ticket back to KIX. Under the Kyoto Station is a huge shopping mall in the basement with restaurants and shops. There is also an impressive, multi-story department store located in the station building. Outside the station there are lots of places to eat.
All this assumes you have a passport from one of the countries that don't need a visa, such as the US. You'll need to get some yen from an ATM or at the cash exchange. The transit hub is on the second floor of the KIX arrivals hall, across the pedestrian walkway over the road. The rail office is on the left in a glass-walled office with green trim, known as the "green window," midori-no-madoguchi. The train leaves right across the hall from the rail office and returns in the basement right under the departure hall.
Except for train tickets, expect to pay cash for things like cabs, subway, quick meals and such.