It actually was really fun overall! I do have a few suggestions though.
1: As far as lines go, yeah, they're annoying, but they're a necessary in a way. The only ways I can think of lowering the line times would either be more leaders, or assistants to the leaders. As in, at the leader's own choice, he could choose to have his-or-her friends using the same exact team to fight challengers for badges as well. It'd be optional, but a choice for those leaders who get swamped or are afraid of getting swamped.
2: Alternatively, to cut down on battle times, I liked the Flat Battle Standard Rules, where you chose 3 out of your 6 pokemon to fight. Now in Black and White you get to see your opponent's team before you choose your 3 pokemon so this could be an extremely fair way to cut down on fight times while still being fun.
3: The Elite Four should have something to distinguish themselves from the rest of the fare. While the Champ has the hat, the Elite Four don't really have anything to tell them apart from trainers. Perhaps a simple 'Elite Four' badge would suffice, since then you don't have to alter those awesome scarves.