The N(ever) and R(arely) going through Brooklyn are the WORST. Poor service, frequent stops due to "congestion" and the most run-down stations in the city.
Just based on anecdotal evidence, the N is pretty good in lower Manhattan and Brooklyn.
As for the R, my preferred method is intensive prayer.
I think that God is the only person who can ameliorate that situation.
I agree that the system is way too Manhattan-centric.