Did a little research on the "recently elite" teams. From 2001 to the present, I came up with eight teams I would seperate from the rest (in alphabetical order): Duke, Florida, Kansas, Maryland, Michigan State, North Carolina, UCLA and UConn. Syracuse was left off the list because 2003 (their NC year) was the only year they made it to the Elite 8 and there were multiple years where they didn't make the Tourney.
Out of this group, Florida is clearly #1 and Duke is clearly #2. After that, it gets tricky.
Three teams on my list, ku, MSU and UCLA did not win an NC in this time period, but did make it to multiple Final Fours. The three other teams, Maryland, UNC and UConn all won a NC, but don't have alot on their resume other than that championsip. All of those teams had at least one year when they didn't make it to the Tourney at all.
Of the six teams vying for positions 3-8, only ku and MSU made the Tournament every year. None of the teams have more that two Final Fours. In regards to Elite 8's, ku leads the way with four, MSU has three and everyone else has two.
Looking at the data, one could make a pretty strong case that ku should be #3 on the list. ku has as many Final Fours as all of the other teams, the most number of Elite 8's and in all seven seasons they've been no lower than a 4 seed in the Tournament. Being at least a 4 seed every year is even more impressive when you consider that UNC, Maryland and UCLA had multiple seasons of not making the Tourney.
In any event, ku is at the very least among the top 6 (I think higher, but it's debatable) programs in this decade. That's elite in my book.
