I have no great issue with a team losing games and winning the All Ireland, the thing is set up so the best team will win overall. Knock out championship is too dependent on luck and circumstances.
The only issue I have with the new system is that it will (as Dermo above points out), involve games that have no meaning in the last round. This will be used as a stick to beat the whole thing with. At the least score difference should be used to separate teams and not head to head, it might keep it more open near the end. But it has a great potential to capture the public imagination.
The one issue from Congress that will come back to bite is letting Christy Ring winners into the championship. It actually means teams are better off in the Christy Ring rather then trying to make it through the preliminary rounds of Leinster. It won't be a problem, until it's a problem (like when they introduced relegation and Antrim were relegated and they realised they couldn't be because they had guarantee of being in Leinster).