There is no doubt that the MOST important differentiator for #1 and #2 in the Coaches and Old Celebrities polls are the -0 at the end of their records. What is a little more dubious is how the computers all sort them to #1 and #2 given that Mizzou's only loss was in OT and Alabama's only loss was on the last play of the game and both losses were against highly ranked opponents.
It seems likely that the new playoff system will be more satisfying only if there is some kind of detailed explanation of why the four teams are selected. An effort to reproduce the "objective" nature of the BCS Standings (which is 2/3rds based on the opinion of coaches and celebrities and 1/3rd based on a non-transparent--and therefore EXTREMELY subjective--computer ranking) is unlikely to make folks happy. But a truly subjective system might be even worse.
Therefore the obvious thing to do is to politic for an expansion to eight games as soon as possible. I realize that if this happens the so-called "BCS" conferences might request an automatic slot for conference champions and for a true playoff to work one could argue that a conference championship game feeding the on-the-field winner of the conference into the playoff is a good thing (in spite of the discussion with respect to the playoff of the "best teams") if the field is large enough.
Otherwise the key thing that is needed is extreme transparency.