short of, say, 5- or 7-game series for each of the 65 matches, which is obviously impossible, the current basketball tournament format is the best system available. letting many teams decide overall superiority on the field of play is always preferable over picking (read: guessing) the two best teams and letting one game decide superiority over all other teams.
the college football championship has its own issues, too. first, i expect that most seasons there are more than two teams worthy of proving that they are the best. second, there have been and will be seasons culminating with a championship game where one participant proves unworthy of selection. third, a college football championship game does not necessarily produce a winner that is actually better than its opponent. truly inferior teams do beat otherwise better opponents.
no system used to determine a national champion is perfect. the nba and mlb championships approach perfection, but they still invite imperfection. that being stated, i think letting multiple teams decide overall superiority on the field of play will always be preferable to guessing which two of many teams are the best.