All D & E Ticket attractions should have an in-theme lounge type area as one of it's queue options. Air-conditioned with restroom facilities, noise cancelling headphones, and even themed activities that act as a compliment to any story-elements experienced in queue. Each entrant would be given either a timed number based on when they entered in line with the standard wait time, or wait for a split-party to retrieve them when they've navigated through.
This isn't a 100% fix, nor is it a new or original concept, but one that is repeatedly shot down on these forums.