In my opinion, there were, for one thing, not meant to be the end of Streetwars (and you "riding under the citadel" is just an awkward skycamera position, before anyone mentions that), and in Retail d3_canals were replaced by revisiting sewers/Under right before Folow Freeman, since both serve as a reminder of "hey, remember how you went through places like this in first third of the game".
Another mystery would be the buggy, was that just a placeholder vehicle to travel through the huge ugly greybox, or was there an idea to have another vehicle section, especially with how Combine steal buggy in Retail and it's never brought up again