I completely disagree with the whole random brackets idea. Much of the charm of a tournament comes from the way the competition heats up with each round, with the matches becoming progressively more exciting, close and unpredictable. Having the "true" finale take place in the first or second round would in my opinion completely ruin the tournament and zap all interest. Instead of having dark horses overcoming the odds and having great runs, you risk having mediocrities make the finals simply due to the dumb luck.
I definitely think IGN did the right thing by actually building its bracket with some thought and care, rather than just making things random. It gave us some interesting match-ups already in the first round, featuring games that otherwise weren't going to achieve much in the contest (like
OoA VS
OoS,
ST VS
PH).
OoT was also prevented from prematurely ending the contest for potential finalists, instead merely taking out fodder. The big mistake was pitting
MM and
ALttP against each other in the second round, surely a result of IGN greatly underestimating
MM. Needless to say, that is not something this site would do.
I should also add that making things random would almost certainly result in more complaints, not less. I mean, what do you think would get more complains,
OoT eliminating
PH in round 1, or
OoT eliminating
MM/
ALttP in round 1? The fact that it would be the result of random draw would (and should) not serve as a perfect defense, insofar as that tournament set-up would not have been inevitable, but instead was the result of a decision (which of course is open to criticism).
The only way a random tournament set-up would have a chance of working would be if
OoT was removed from the main contest, and instead faced the tournament winner in a bonus match/grand finale.
MM or
ALttP can conceivably be upset by a dark horse in the first or second round.
OoT, not a chance. Also, the final standings after the tournament ends should be based on indirect strength, not simply how the games finished in the tournament, considering how unfair that would be to the unlucky games.