The biggest indictment of the current system was self-exposed day one.
In the first season of CFP, going into "conference championship week" Ohio State was on the outside looking in. Third ranked (by CFP) TCU beat Iowa St 55-3 and dropped to 6, leaving the door open for OSU. I really am not sure what is more absurd, that TCU's thrashing of their in conference opponent in the conference title game was not sufficient to keep them from dropping more than one spot (which would have kept them in) or that it took some alternative mathematics to allow OSU (who in the playoffs demonstrated that they were clearly better than the three schools selected ahead of them) to join the party. What may be most bizarre is that Baylor (who did not play) somehow jumped TCU in the last ranking
As far as this year goes, when Alabama beat Florida (yes, the Florida who just fired their head coach) in October, they did so because a) Florida missed an extra point after their first touchdown and b) because of that miss, had to go for two late in the game (after their last touchdown) in an attempt to tie the game and did not succeed. It wouldn't be much of a stretch to believe that if the first extra point was not missed, that would have gone into overtime. Would Alabama be any different on the field today if they did in fact need overtime to beat Florida? Would the opinion of Alabama as far as being deserving of a spot in the CFP have taken a hit if that game did go into overtime?
The thing is, you cannot base it solely on who you believe would win a head to head game as a) the opinion could be wrong (nobody would have selected OSU against Bama the first time around) and b) it is possible that an extremely strong team could have stumbled, messed up or just not cared enough during a game or two during the season and if this is based solely on who you believe would win, there then would be no consequences for said mishap. That goes against the spirit of competition.
My biggest problem with the CFP is that while claiming they want to find an true champion, they are just continuing the subjectivity of the results (disguised as a true playoff) while having eliminated the closest thing to an objective selection (the computer rankings from the BCS) which was eliminated solely because it wasn't gaming the system against non P-5 schools as completely as they wanted.
Cincinnati warranted a lot more consideration for a spot last year than they received and represented well against a very good Georgia squad at year end. The same Georgia is now clearly the most deserving of a spot at this point but Cincinnati, after doing all that it could to date still is at risk of being eliminated, not due to what they did on the field, but rather because they aren't yet a member of a conference that the committee is willing to give a spot to.