Our youngest son has disability-related needs that make crowded bus transportation difficult for him. So this is different from OP's concern, but I've appreciated all the various suggestions on this thread, and thought I'd throw in a few of our transportation strategies. Pre-boarding on southwest helps with the flight,
DAS and resort breaks help in the parks and noting a request for a booth on ADRs helps with dining. But Disney disability services has always told us there is no specific system in place to address his needs regarding transportation, so we've come up with a few things we can do on our own to accommodate. (I love the idea of a DAS for transportation - a separate waiting area would be great.)
First, as others have mentioned, we try our best to travel during times that will be less crowded/busy - both in terms of time of year and time of day. For the boats, we hang back on the dock if at all possible so that he's not in the middle of the line. At WL, YC, BWI and CR, that's further back on the dock. At MK, that's near the few benches that are out on the dock. We'll never be first on a boat, and sometimes I'm concerned about missing a boat/not fitting in the next boat, but it gives him needed personal space. The monorail is OK, but we always try to find the least crowded queue area to wait and hang back a bit there, too. The bus lines are tough. I agree it's more space than a traditional line, but for our little one, it's still a confinement issue. So we try to create some space for him by standing back a little around him to create a circle of air/space. And we let him sit on the ground with that space around him, if he needs to sit. Yeah, I know it's really yucky, both because I know that and because another guest decided to tell me that once. But we wash his hands immediately afterwards and clothes go into the laundry, and it's better than his disability-related response to feeling "trapped," which isn't good for him or for anyone else. (That's how our oldest son responded to the commenter while I was too stressed to respond.) On a crowded bus, we try to create the same circle of space/air around him if possible. And if it's not, then we all use our best distraction/comfort techniques for the ride. And he keeps a small, light blanket in his backpack so that he can put it over his head and block out surroundings when necessary. Now that I look at this, it seems like a lot of hoopla, but it's just habit now - things we do while waiting and chatting about the day, etc.
So again, I wish I had suggestions for OP's specific concerns, but I thought I'd throw it out there in case it's helpful to others. And I'd welcome additional suggestions!!!