how does the NY MTA System assign letters to trains, and why are some letters skipped?

Answer 1

The person above is mostly correct. The MTA hasn't really skipped letters, (some have yet to be used) but there have been train lines in the past, which used certain letters and numbers, but have since been discontinued. The only letter to be used multiple times is the "S" train -- which is the designation for the shuttle train. There is a Times Square Shuttle, Franklin Avenue Shuttle in Brooklyn and Far Rockaway Shuttle in Queens.

I know off the top of my head that there used to be a T, 8, H trains. In fact under the old system, for the BMT and IND trains, local trains used to be designated with double-letter designations.

The E was EE, the R was RR, the G was GG.

Answer 2

By now, most of the alphabet has been taken. The only letters that are not used are "H", "I", "P", "T", "U", "X", & "Y". The Interborough Rapid Transit System (IRT) uses numbers. The Brooklyn-Manhattan Transit (BMT) & Independent Line (IND) use the letter system. How the letters are selected by the IND & BMT could probably be found at the MTA web site.