Exactly, this is how I felt. I think the MTA would want their newest Subway Cars, on their Express routes, as they require the most capacity, along with more reliable service. The R142/A's would still be CBTC-capable, and would be more than sufficient for the . Since there would likely be some leftovers, they can go to the .
The , like you said, are the longest, and most used of the IRT lines, and being that they do share a fleet, it would make sense for them both to run R262's.