We never had an issue with rain, just lightning! And that was also for the safety of the guests. It's not so much a lack of covered waiting area, but more an issue of guests, as well as CMs, having to walk backstage in the open. It would be pricey to start making covered walkways from inside the park, to the outside, backstage areas.
I think the issue was more one of lack of use. I don't think we were ever on a bus with more than 8 people. If they started using vans, then perhaps it would have been more profitable. The other issue was that some people thought they could just walk up, and be put onto a bus. But, the buses ran on a schedule. And each park had a different time frame. So, if you got to the loading area just after the MK bus left, you had to stand and wait for half an hour! And those buses didn't sit and wait for stragglers. If the bus schedule had the bus leaving at 2:10, that's when the bus left. If you arrived at the check-in CM at 2:05, you didn't get on the bus. You had to be checked in, and then led backstage by another CM. Once that CM left with a group, that was it!!