My feeling is this. Unless you're really about the night life and clubs, Kyoto is the way to go for the majority of the trip. I usually end up arriving and departing from NRT however. This is because the fares to and from KIX are usually a lot more for me. Your millage may vary depending on where you're flying from. It certainly is quite nice to start at NRT and end at KIX when you're doing the classic Tokyo/Kyoto combo.