I've got petty complaints and things, but here are the big hitters:
To beat a dead horse: schedules. I'm fine with them not being included in the packets, provided that (a) it's posted far enough ahead of time and (b) the schedules are placed online in a format easy enough to print off what we want. If I'd known they weren't going to be in the booklets, I'd have jotted down the room info for the panel I went to beforehand.
Black and White Ball: I know the smaller room was out of the hands of staff this year, and we wound up taking a look at the line and changing our minds about going (sadly, but ...). However, one thing I really wish could be done is to NOT schedule it against the Masquerade, or if so to lengthen the hours so that people can theoretically do both. It's hard to be torn between the two, particularly when trying to support friends who are competing.
Masquerade: Long opening acts were LONG -- and didn't help the Ball-Masquerade time conflict. I wasn't timing last year, but I seem to remember this year's preshow (band + karaoke winner) running something between 45 minutes to an hour. As bitchy as it sounds, I come to Masquerade for the cosplay; maybe consider shortening the opening acts and saving the bulk of it for intermission?
And speaking of: had there been a capacity cap reached such that they were turning people away at the doors for the Masq? It was odd with seeing quite a few empty seats, but I don't know what the building capacity is. Just curiosity.
Dead Horse #2: Prereg line on Day 0. It's gotten more ridiculous, and surely there's something that can be done about it (and, as noted, about how damned hot it gets down there) -- longer hours, more open stations, something. We wound up looking at the line and changing our mind (crawled downstairs early the next morning and managed to get through in under an hour).
Overall, I really do enjoy Fanime and I plan to come back, but there are definitely opportunities for improvement still.