The ride was designed that way for theming, hence the unload station having the cracked walls (from after the earthquake). The no loose items policy also helps speed up the loading process, well was meant to anyway. But once the doors open and guests board a train can be dispatched generally within 30 seconds with 2 loaders that are on the ball.
The ride however is not efficient at all with 1 train, and I'd say was designed to run pretty much all the time with 2 trains in mind. IMO what would have made sense is having 3 trains so that the ride can always run with 2 trains as required and only drop down to 1 train in the very quiet months (End of Jan > End of March periods).
Superman with 2 trains and a dedicated sorter can easily dispatch between 25 and 30 trains a hour giving a capacity of 500 - 600 per hour which puts it not that far below Scooby Doo on a good day (which is about 700 a hour). Hardly a bad design, just not utilised in the best way at all. When the ride first opened I'd say it was actually getting closer to 35 trains a hour with 4 loaders, a sorter, entry host and 2 unloaders and ran very efficiently. However I think the 4 loaders and 2 unloaders was overkill and clearly the park did because after opening year it was cut back to 2 loaders, entry, sort and unload for 2 train ops.
I swear though... if they ever cut that ride down to 3 staff again (Load 1, Entry, Load 2 / sort / unload)... that was the worst decision they ever made and lucky it only ran for a few months like that when they realised 8 trains a HOUR was absolutely horrible.