Using the local to go to Manhattan from Brooklyn (& vice versa) is definitely not habitual. In the very few times I did so, I noticed something worth mentioning. As the R line passes through the Cortlandt street station, it slows down. If your not familiar, this station is the one that used to serve the WTC towers and adjacent areas. When the train passes by, you get to see the interior of destruction (or construction, but realistically rather than pessimistically, I see it as the former). It's a sad moment. I find it remarkable that the train slows down, it's a strong statement for NYC to make: as quick as the trains have to go, they slow down in respect and reflection of what had happened at that site. I prefer to think of it as that, though maybe the reason is to not affect the construction on ground zero (a less likely possibility since the trains speed up as soon as they are away from the edge of the station).
Apparently, the MTA was planning to reopen the station this year, but delays happened.