One thing that a smaller convention, AnimeUSA, utilizes is to dedicate a panel room to a topic. IE- all cosplay panels are in room 1, industry panels in room 2, web/fandom panels- room 3, international guest- room 4, domestic guests- room 5, etc. It makes it easy for attendees to find their favorite panels, and it prevents similar topics from being scheduled at overlapping times.
I've staffed conventions before, but not in the paneling dept. I'm not sure how Otakon panels are scheduled, but it could streamline the process.