I did not like the subways at all, I think they were too small, too similar and generic and yeah they freaked me out. I do not want that back.
However Blackreach was just plain crazy, if there was anything similar in Boston I would all support it. I think there should really be more to a subway system than what we saw in Fallout 3. More and larger halls, for example. Or they could take some inspirations from the Moscow subway. Anyway, the biggest thing that needs to be done is that it should all be connected, not loading screens. Basically like Blackreach.
As we speak huge dungeons, the huge skyscraqer you could see in the Demo might be a candidate as well, not that spectacular, but could work out. I think every RPG needs some huge place that takes hours to explore.