Sure, there will always be something to complain about. Some basketball teams complain that they get left out of the 65-team tourney because they ended up being #66. But you know what? Nobody really pays much attention to those complaints, because there are plenty of opportunities to make the postseason, and they all knew what they needed to do to make it: win their conference.
A 16-team tournament that includes the 11 conference winners is a solid, if imperfect, system, because it lets all D-I teams know that you can make the tournament and have a shot at being national champion if you do the one thing everyone already knows they need to do each year: win their conference. Don't win your conference? Too bad. But at least in the 16-team format there are 5 teams that get a second chance. Anyone who complains that they aren't one of those five teams just needs to shut up and win their conference.
It's not rocket science, and it's not perfect, but it's exponentially better than the current BCS. We cannot allow perfection to be the enemy of the good here.
Go Utes!