This is already true of the WC anyway, so imo it's not that big a deal. Some teams will simply be at a slight disadvantage, but the benefits probably outweigh the negatives.
I'd like to see them simply eliminate all the divisions, drop the season to 150 games, and let the top 16 teams into the playoffs. Let everyone play each other 5 times (5 games and days in a row), with the home/road series swapped each year.