There are TONS of train lines. (as seen here: http://www.mta.info/nyct/maps/submap.htm
) and probably others I forgot. They're 24 hours, which rocks, and during rush hour most trains run every 5 or so minutes. You never really have to wait long for a train at rush hour.
The problem is that they run trains 24 hours, so whenever they have to update something, they usually do what's called a "service change." They'll post a note up telling you when it happens, but sometimes they don't post the note up until last minute.
There are like millions of service changes. One, they might just move one train onto another train's track for just a mile or so. (like putting one of the 8av trains on 6av and confusing the hell out of you). Or they'll run one of the local trains on an express track (when this happens, there's a note telling you to take the train in the opposite direction and then switching over to your direction at an express stop). Sometimes, they'll just shut down a number of stops and replace the train with a shuttle bus.
Also, the trains are all crooked and they often run different routes at different hours. For example, the M train goes through Queens and Brooklyn into Manhattan and then turns and goes into a lower part of Brooklyn during rush hour. But during the day, it stops at Manhattan. And at night, it doesn't even go to Manhattan.
Basically, you just have to KNOW the train lines, which takes not too long. you start with the one you take to work/school and you learn the rest over time as you need them. Once you know them, MTA gives WAAAAAAAAAAAAAAAY better service than Septa, even with all the hassles.
It's cheaper too, and the busses run a lot more often.