You're never going to get people to agree on anything quantifiable, because everyone is going to bring an agenda to whatever type of scoring you come up with. But your numbers don't seem too bad to me. I would make a few changes, using this for the truly elite programs:
NCAA title: 4 points
NCAA runner-up: 2 points. You played for the title, and winning games in the FF is hard. Ask John Calipari, ask Tom Izzo, ask Rick Pitino, and most of all, ask (if you could) Dean Smith.
FF: 1 pt
Sweet 16 or Elite 8: 0 points. This is sort of a baseline level of achievement for elite programs.
1st OR 2nd round loss: -1 pt. If you're an elite program, something went wrong if you can't win your 1st 2 NCAA Tourney games.
Missing the tournament: -2 points. Big fail, and it makes no difference what happens in the NIT.
Using that system, UK gets a 6 since Cal's been here, and so does Duke. Which strikes me as about right. Given where UK is at right now, I'd take the 2 titles, but in the broader historical picture, you can't just dismiss the fact that UK has won 5 more NCAA tournament games than Duke in Cal's 6 years, or that UK has twice as many FF appearances.