I agree that the audio issue was something to be addressed, but I'm not sure we could get wireless mics to hand around.
I think the unpanel format would have worked much better in a smaller room, I hope that next year Fanime will open up of the other conference rooms available downstairs, away from the Video room and hallway noise.
For a big room I'm thinking about a "Congressional Hearing" format. The idea would be that there would be one to three moderators, taking the place of the Congressmen, and several panels of 3-5 people picked from the room who would come up and "give testimoy" for five to ten minutes on a particular subject.
The way this would work would be that the moderator would call for a panel on the subject, for example "Fanfiction.net", or "Mary Sue", or "Self Inserts" and those who wanted to be on that panel would raise their hands to be selected to be on that panel. They'd then go to the front of the room to be sworn in, and to use the microphones to talk about that subject. The moderators would ask questions, and repeat audience questions so that everyone could hear. Panelists could "testify" under multiple subjects, but preference would go those who had not been on a panel yet.
I know this makes it harder for the shy atendees to participate, but it would mean that everyone could hear everything.