It's Alabama and Clemson or vice versa...then everybody else. They get in because they are better than everyone else. It's clear and obvious. I am for an expanded playoff too, but to say it isn't fair or flawed because Alabama and/or Clemson get in with blemishes is kind of foolish.
The playoff system as it is now is about putting the best teams on the field against one another. There is currently no other team in FBS at their level. If people don't like it, they need to beat them...and keep beating them until the tide turns.
It will happen eventually, but for now, we're stuck with two great programs and then everyone else. I'm sure this is how people thought of Nebraska and Oklahoma or Nebraska and Miami in their hay day.