Regarding the MoM as a set piece in a theme park, I'd personally like the main hall to be an area you can explore. I think Hogsmeade taught them that guests may not want to ride, but they will want to take the photo of the location and visit them, hence why so much of Diagon is places to explore.
So bearing that in mind, I'd like to see it set up like a "pavilion" with a ride area themed to whatever, hydrolator type entry via floo or telephone booth, leading to the main hall, some visuals of the intricate elevator system, maybe gift shop and employee commissary. Maybe the entry to the ride is the department of mystery area and thus the queue is all of the various bits of that which show up in the books (there's a lot of rooms Harry and friends try before finding the prophecy storage.)
But that version would likely have the "good" Ministry as the set piece for the main hall with the magical sentient beings fountain.
So as an alternate, it could start in the "bad" ministry with the muggle oppression fountain - which would logically allow for things like Umbridge's office, and also the courtroom thingy. Then during the ride, as in the film, the main hall gets destroyed as we defeat the villians and watch the epic battle. Then as we've seen in Fantastic Beasts a bunh of skilled aurors can repair a place pretty quickly, so when we disembark we exit via the "good" main hall of the ministry with the magical being fountain instead of the bad one.
Just my thought, no idea what they'll go for - but I do know more recently rather than starting from a point of "what story do we want to tell?" creatives at UC and WDI start from a sort of "vision board" of things research has told them people are expecting to see or have listed as "must see" "must do" as part of an IP. It tells them which locations and characters are important and guests feel are must-haves. So the above sort of fills out my personal must-haves.
I think it's safe to say most people's must-haves list for MoM includes prophecy storage - the subsequent destruction of it - as well as the main hall, and on a smaller set pieces note.. the veil.