The question of which team deserves more praise -- the Ohio State or Kansas that dominated the regular season but didn't make the Final Four, or the UConn or Butler who struggled throughout the season but got hot at the end -- is highly debatable and perhaps not possible to answer. But what is possible is to make a distinction between types of greatness, and to recognize that greatness can happen at any time, not just the end of a season.
For all the problems the BCS has (and they are myriad), I think that one game does a better job of determining the champion of the sport than the NCAA basketball tournament. And for all of college football fans' sturm und drang about the BCS, we hear not but mere peeps about the NCAA tournament's "inverse BCS" problem.
While the BCS eliminates teams that may have a claim to be the best from consideration for the "national championship", at least the team that does win will also have a claim to be the best. In the NCAA basketball tournament, so many teams participate that are not even close to the best that very often, this year included, upsets will occur and a team like Butler or UConn will be in position to be named "national champion." These are inverse but similarly troubling problems.