4 titles in 15 years is awesome - but I still don't think that alone qualifies them to be places in the same category as UNC, Duke, Kansas, Kentucky, etc.
As Rob mentioned their last 2 titles came out of nowhere. I don't think anyone thinks UCONN was the best team in the sport during their last 2 runs. They got hot at the right time and played great in the tourney. Which doesn't diminish the achievement at all, just shows that as exciting as the NCAA tournament is it is probably the playoff series that is least effective at determining the "best" team.
Not at all trying to hate on UCONN, I have nothing against them particularly now that Calhoun is gone. Just think we place a little too much emphasis on what happens in the tourney. As was mentioned, St. Joes had them beat in round 1.
The biggest problem for UConn IMO is their conference. If this were football, you probably would've seen more conferences trying to get them.
Of all the sports championships that have a lot of a intrigue, this is probably the least indicative of the best team like you said. It's one-and-done and played at all neutral sites. This is a team that needed OT to get out of the first second round after all. Would a playoff series, be a more fair way to do this, sure. You also wouldn't have 68 teams and the upset potential would be a lot less. Mercer would have a much tougher time beating Duke if they played a best-of-3.
In terms of placing too much emphasis on the Tourney, that's the goal at the end of the day like in any sport.