They were absolutely great. But UConn was better. I think there's this idea--and you yourself suggested this something like this, if not the specifics--that, if the teams played an NBA Finals type series, Duke would win in 5 or 6 games. The pushback is that UConn was better: not just on that day, but really, actually better, and would win a best of seven series.
Everyone agrees that the Celtics and Lakers of the 1980s were great. But in the years the Celtics won (1984), they were the better team. And vice-versa (85, 87).