It may suck initially, but I assume they will update them individually. If I won't have to download a 90+ page document every time five new questions are added about a single splatbook, I think it's a great idea.
Because now its more difficult to do a word search for something in the FAQ. And it makes it more difficult to reference the FAQ when you are in a rules 'discussion'.
Hey, do you guys think Wizards would get pissed off if someone combined all the individual FAQs into one PDF and offered it for download? Probably, but if not, that would be cool.
While others may like the individually divided sections of the FAQ, there are others like me who prefer to have them all compiled into one single document.
It would have been courteous of Wizards to provide such as an option.