One of the hardest parts must have been designing the transitions between one environmental reconstruction and the next. A transition has to feel continuous and not abrupt, but still convey a sense of change so that all the environments don't bleed into one. It also needs to save space wherever it can. The very best are so subtle that you don't even notice them.
My favourite transition is here, between the Ontario Street and the Canadian Prairies.
Did you notice what they did? I didn't until last year.
Take a look at the furniture store on the Ontario Street, and the railway car in the Prairies.
They're the same object! It's just decorated differently on each side.
You don't notice because you're looking at the CPR ticket office and the Govan train station. This interrupts your perception of the object. By the time you turn back around, you're in the next streetscape already, so you don't perceive its continuity.
And if you do happen to look at the side of the object, they've got you covered there too:
This panel on the driving of the last spike slows you down, once again distracting you from noticing the transition. (I especially like this view because it's Ontario on one side and Saskatchewan on the other.)
And by making one object stand for two, they save space too.
If you like this sort of thing, check out the post "The Awkward Transitions of Disneyland!" on the wonderfully detailed theme park blog Passport to Dreams Old & New. Theme parks were one of the reference points used by the Canada Hall's designers.