It's so the No. 1 seed doesn't face someone from the same division in the LDS. From the MLB.com postseason format FAQ:
Are teams reseeded after the Wild Card Series?
No. The No. 1 seed will face the winner of the Wild Card Series between the Nos. 4/5 seeds, while the No. 2 seed will face the winner of the Nos. 3/6 series. This ensures that the No. 1 seed won't face another division winner in the Division Series round while still preserving the bracket system.
I guess I don't understand how this format prevents the No. 1 seed from facing someone from the same division. Couldn't an intradivisional opponent be a 4 or 5 seed? It sounds more like a rule meant to prevent NYY-BOS, NYM-PHI, LAD-SFO or even CHC-STL or LAD-SD matchups in a five-game series versus the seven-game LCS so that TV gets more potential games in those large markets.
I'd rather see them reseed after the wildcard so the No. 1 team plays the lowest-seeded wildcard survivor regardless of what division they're from. If I'm the No. 1 seed, I'd rather play the 6 seed if they advance.
David