LIRR and Metro-North are actually quite fantastic. You can now buy tickets on your phone; the trains run on time for the most part; and they're fast, comfortable and fun to ride.
The LIRR does not run the trains on time for the most part. The branch I take every day has an on time percentage of 94.2% for last month and six minutes late is considered on time. From personal experience, extremely long delays (30 minutes) or canceled trains are about a monthly occurrence.
Also, while you can now buy tickets on your phone, they still use a very labor intensive process of having conductors walk up and down the aisles and check tickets twice per trip. That contributes to the LIRR very high operating costs.
I'm more up on the situation in Boston than New York but I doubt the conductor checking the tickets is really that high up there on the list of reasons why both systems have financial troubles (at least except to the extent it enables fare evasion, which is apparently quite common).
