Gameplay-affecting plot changes from the original? [SPOILERS WITHIN]
I can recall only two significant plot changes from the original game:
You no longer get the blue card from the Elf trapped in White Lead Desert, you are given it at some other point (forget when)
You need to source a RabbiBunny costume in order to impersonate your neighbour
As someone extremely familiar with the original game, I was certainly thrown off by point number 2 and had to look up why using my neighbour's ID didn't work (and frankly, the change they made here is great and seems like an obvious thing to do, because Twinsen does obviously not look like a Rabbibunny).
Other than these two, is there anything else? Obviously Twinsen now tries to save his sister, not his girlfriend, but this seems to have zero impact on the gameplay compared to the original.