The issue is the rather arbitrary way that the committee appears to apply the criteria. In ranking some teams WIN% is the most important criterion, and SOS is secondary. In other cases SOS is more important and outweighs WIN%. The real problem is the lack of transparency. In hockey there are two regions (we are a small sport), an 11 team field with 8 Pool A leagues and 3 Pool C bids. (We have one league with only 6 teams, and no independents, so there is no Pool B).
The last couple of years what has happened has been the case that there seems to be a lot of game playing going on. The regional rankings have been manipulated to help one region get the upper hand in the selection of Pool C slots. A team mysteriously appears at the bottom slot (16th in the East or 8th in the West) that enables a borderline candidate's resume for the last Pool C spot to improve. The real problem is that in some ways hockey traditions and practices are different from other sports, and the problems in selecting the field really started with the advent of the Pool system.
Before that started, there were some weak leagues that didn't get auto bids, and the number of at large bids was larger. We all understood who would be in an who would be out - the process was transparent. With the granting of Pool A almost automatically to any league with 7 or more teams, we have gone from 5 auto bids to 8 - The ECAC Northeast, MASCAC, and MCHA have all recently been given auto bids, and two of those leagues have exactly 7 members, and are very weak. When you lose almost 20% of the field to accommodate auto bids for teams that have no chance, it squeezes the Pool C choices and makes the whole process seem very political. The MASCAC + ECAC NE totaled 13 teams, and when the MASCAC was formed, they ended up with 7 teams by taking 6 ECAC NE teams and "stealing" one from the ECAC E. The net result was the loss of a Pool C spot at the cost of adding a team with little chance to advance. In other sports, I'm sure that happens as well (Norwich playing in the Football tournament a couple of years ago would be a good example), but the percentage of the field that is affected is greater.
My rant I guess really comes down to the "one-size fits all" approach that is used in setting the field.
I apologize for the long rambling rant