As shane points out, the bye before the finals shouldn't really favour one team over another in the first final. It might slightly disadvantage teams than had locked away a top 2 or top 4 spot before the final round, and could have rested players where other teams fighting for a spot couldn't, but that's a little at the margins.
Where it would have an affect is at the prelim final stage, where the lower-placed team has had a rest, then two good hit-outs leading into a prelim (seemingly an optimal preparation), facing a team that has played once in three weeks (potentially a less optimal build-up). Coaches often say players are creatures of habit, so I imagine going from playing weekly to one-on, one-off could have an affect. It's not a fact this favours the lower-placed team, but if the coaches and players suggest it would be a disadvantage to play relatively less footy in September coming off a bye, I don't know people could argue they are wrong.
If all you want is a more even finals one through 8, then I guess handicapping the top 4 teams serves that purpose. But If a premiership season is about giving a trophy to the best performed team over a season, then I think a system that heavily favours the top 4 is ideal.
But I think the Bulldogs were a bit of a red herring. They hit a purple patch heading into the finals the way we did in 2013. The difference is theirs lasted one more game, and they weren't playing they reining premiers on their home ground. I'm not sure how much it had to do with the format.
