Actually I think the big reason was DQ's in both the Melee days and Brawl. For Brawl, for example, we only had 20 setups for a 250 person tournament and averaged over 180 people over the 5 MLG events. It was straight double elimination, but even then that would have been impossible to do without adhering to a very strict time schedule.
I DQd the #2 overall player in the country (Ally) out of winners and a few other top 20 players in the same tournament for being late. Most TOs will not have the guts to do that, and the few that have done it (myself, Plank, a few others) have gotten flak because enough people side with the top-players for bad reasons that is makes things difficult. Sigh.
But really, almost every single large tournament I've seen can trace their issues with time to not DQing people. Setups is an issue, but as a TO, you know the amount of time you have to work with, and you know the amount of setups you have to use. Therefor you should be able to derive a schedule that will finish the tournament in that timeframe, failure to do so is either bad/terrible planning or matches running longer which is usually (entirely) do to players not showing up on time.