So the Japanese method (though they don't use line numbers)?
Osaka has Line Names, Latin Line Letters (Markers) and Line Numbers for internal use. All the stations are also numbered along the line, so for example Hommachi station on the Yotsubashi Line is Y13. These are included in announcements in English as well as Japanese, and probably very much appreciated by non-Japanese speakers!
Danger of using Line letters is that you run out! Can see why line numbers are more popular, and would be the go to in places without an alphabetic writing system.
Or you could end up like New York, and have to change them all multiple times. Most people in New York still refer to lines by their name, like 8th Avenue Express (A). But the letters and numbers are still pretty important for distinguishing services, particularly on the map. Personally, I wouldn't gain much from say, a letter and number to distinguish particular services e.g. M1 for Metropolitan line Aldgate - Amersham, but others might, particularly if they don't understand English well.