The arcade scoreboards are accumulating some cruft, for sure. I wouldn't be against flushing them out every so often. My only thought is it would be kind of cool to keep an "all time highest score" noted somewhere, just for recording of the epic wins that may be unlikely to be repeated. It certainly doesn't need to be live... It could even be just a little flat text file tucked away somewhere. Each time before the high scores are flushed, check if the current high score is higher than the "all time highest score" and update, if necessary.
But I think a main arcade reset every so often, and letting the live scoreboards, trophies, and "champion" designations be for the current leaders of each game is a good idea. It is kind of funny how all the trophies gravitated to be divided up between a handful of people. As X-Ray said, I suspect there will probably be a lot of the "usual suspects" dominating their respective games again after a short while... But in the meantime, it'll be a fresh slate for everyone. Sounds like a good thing, to me.