This kind of thing has to be expected now a days, even if they had put a limit on the orders. If the order limit was 6, and assuming that the majority of people who were able to purchase bought at that limit, there would be about 100 transactions that would be able to be put through.
Remember when Ellusionist had their Red Artifice deck released and the whole website/server crash deal? I remember reading that they were experiencing roughly 600+ page loads a second, so even if a portion of those collectors wanted the Magi-Con v2 decks, there would be more than enough people to buy out the remaining stock in < 1 minute. In my opinion, no matter what D&D would have done, there would be people pissed off, there is no comprise that can satisfy all.
As for the marketing that D&D has done to sell the decks, I believe it was fair and the hype for the sale was really generated from the community rather than a hardcore marketing plan by the Bucks. Simply put, all D&D did was state that they had a few more decks going to be released ( Which either planned or not because of the attendance to the convention ), and stated what time they would go on sale. There was not marketing of these decks stating they were the best decks ever created and you must buy them in order to live a happy and successful life, the excitement for these decks was pretty much self created by the community ( and in my opinion by people knowing that the aftermarket value would be pretty good for the reseller ). I mean, what else is D&D going to do?, just secretly put the rest up for sale in the store without saying anything? I bet that would piss just as many people off, if not more.
I don't understand much of the complaints by members of the community for missing out on a deck, everyone has roughly the same opportunity (internet speed, ect..) to purchase decks for their collection and it is not the end of the world if you don't end up with a deck you wanted, just move on.