Certainly over the course of a season, the best teams should have the best records, or be the hottest come December. In real life the occasional wild-card team wins the World Series, but a baseball team gets a seven-game series. A fantasy football team often gets one game, and if your studs don't show up, well, Merry Christmas. In one of my leagues the team that scored the least amount of points in the regular season went 7-6 and slipped into the playoffs. They're currently beating the top seed by 18 points.
Best answer I can give on sticking with a head-to-head format and fairly deciding a winner is to go with two weeks per matchup, not one. The best team can still lose, but that team has a better shot to recover from his nasty Week 14 and put up 150 in Week 15 and still win. But it's not an excuse. I lost a league in which my unbeaten team was averaging 110 points per game. It got 52 this week. Not much you can do but play your best and hope.