I'm not sure I get the uproar. Now, if two teams are tied, there's a play in game. Obviously the two WC teams won't necessarily be tied, but it's not like this is something new. Hell, despite the collapses of ATL and BOS last year, we still could easily have ended up with a play-in game in each league - which is what we'll have now.
Besides, I've been hearing whining for years about how the system isn't fair because it's so easy for WC to get hot and win it. Now, they either have to waste their ace in the play-in game, or save their ace for the ALDS, which they may not get to.