You make some valid points but wildcard teams have won the Super Bowl. And the World Series. Teams improve over a season and some peak at the end. Others have critical injuries early and get healthy in time for playoffs.
Why should a team that "peak at the end" win a championship? Is that a good thing? Doesn't it make more sense to reward teams that have had an overall better season as a champion as opposed to a team that has a couple of good games/weeks?