1 and 2 seeds both get byes. The 3rd division champion doesn’t, and many years it is somewhat likely that the top Wild Card team is better than the 3rd division champion.

Look at the NL this year. The Cardinals are the 3 seed, winning the NL Central with 93 wins. The Mets are the 4 seed with 101 wins.

The 1 seed Dodgers get the winner of the Mets-Padres while the 2 seed Braves get the winner of the Cardinals-Phillies.

Seems re-seeding, or choosing your opponent, would fix this. But MLB wants the logistical clarity of set brackets.