Threading system
When a thread gets too long, the threading system seems to break down. Hitting a post on the list on the right generates a large section of the thread, not just the post. Hitting reply creates a reply window, but the posts above are not the ones you are replying to. I have to either print the post or open it in a new window for reference.
Long threads were a bitch even in the old system, but now without the color-coding and such, it's bitchier.
Of course, no one is forcing us to extend the back and forth into infinity... :)