Half the staff not knowing what the other staff is doing. Basically the 'largest Anime Convention' was still being run by a highly understaffed and mostly volunteer group. FOr an event that is pulling 45,000-70,000 people, usually you either have a dedicated TRAINED event contractor running the show or you hire out to a company who knows what the hell they're doing. Anime Expo does neither, running it like they are just another small-time expo at a local hotel expecting 5,000 people to show up. Hopefully they have hired out in the last year or two but for the 5 years I went...not the case.
They also don't know what market they are attracting. Or at least, they don't care. They put dubbing celebrities as the 'focus members' on the seiyuu panels (good old Crispin Freeman used as many times as they can), the 'contests' are run by complete bias amateurs and the show floor is a madhouse where anyone could come in and steal, assault or just frankly blow up a portion of the place if they wanted to.
The whole 'Expo' is more of a loosely controlled chaos, more so an exibit for the American Distributors and their wares and for small time Anime hawkers to shuffle in and try to sell as much as they can and get out then being anything to 'further than Anime industry in America'.