Actually, I disagree that the NL Central winner (Cubs) is getting the shaft because two division opponents can't meet in Round 1. The wild-card is (and should in my opinion) automatically be the #4 seed and not be seeded higher than a division winner, thus the Cubs are playing exactly who they should play in Round 1. This is how it is in all sports. Otherwise, don't even bother with divisions because winning your division means nothing.
Now - if the Phillies had the best record in the NL and had to play the Mets instead of the Dodgers, then you'd have an argument. That rule should probably be removed.
If you recall, it used to be WORSE when they first went to the wild card system. The first three years of the wild-card system, they based the first round matchups on a rotating system where one division winner - regardless of record - would automatically be a road-team in Game 1 of the first series and not play the wild-card, even if they were not in the same division. Now THAT was stupid.
"The government cannot give to anyone anything that it does not first take from someone else"