If people should be mad at anyone for this situation, shouldn't they be mad at nintendo ( or whoever is behind making this book ), for making the damn thing limited in the first place?
The company in question is Dark Horse. Nintendo did not publish this book, they licensed it to Dark Horse.
LEs with Dark Horse are notoriously screwy. And by notoriously screwy, I mean the Hyrule Historia LE and the less known but even bigger mess that was the Amano signed edition of The Sky. In the case of the latter, Dark Horse never stated the final number of copies until after launch (might have been because they had to wait to find out how many Amano was willing to sign), and as a result virtually every store oversold it. People got screwed, and now it's going for 800$ on second hand retailers. But in that case, the fault was purely on Dark Horse, they never told anyone what to expect, allegedly.
Now with Hyrule Historia LE, Dark Horse said they were incredibly clear to retailers about their allotment of copies, but some still oversold (Barnes and Noble seemed to be the biggest offender here, with Amazon goofing a little too). Retailers really do need to look into something like a separate system to deal with sales of limited edition items. Scalping is a huge problem that retailers
can at least help to reduce by enforcing copies per address limits. I've seen it done it with hardware (namely the Wii and DS back in the day), so they should implement those systems here too.