From 2012-2015, the 1 and 2 seeds received byes to the semifinals. The championship games each of those years were:
2012: #3 Ohio over #1 Akron
2013: #1 Akron over #2 Ohio
2014: #1 WMU over #2 Toledo
2015: #2 Buffalo over #1 CMU
In six years of the current format, the #1 seed has only won the tournament once, and only reached the championship game one other time. The format certainly doesn't preclude the top seeds from winning the tournament, but there was a clear reward for the top two teams during the double-bye era, given the championship game was #1 vs #2 in 3 of the 4 seasons.