It would still likely be quite expensive to retrofit any kind of CBTC equipment onto a SMEE. (That is why the R62/As and R68/As will not get the technology installed.) Only small sections of the system are currently using CBTC and the rollout of new sections is going very slow. (I would love it if the MTA could get their act together and speed up the roll out.) Also, the CBTC equipped sections all receive a new backup fixed block system that is currently used for work trains, and will likely be used for museum trains in the future.
Speaking of Patco and signals, why did the never install ATC / cab signals on the subway unlike the rapid transit lines run by the CTA, MBTA, SEPTA, and others?
Another system (outside the country) used to have a "rain mode" on all their trains that improved performance in rain but slightly reduced acceleration and brake rates. The mode would also occasionally disable dynamic brakes.