There's a source that I can't find that explains why the L in particular so bad. It's basically that most subway lines (e.g. the 2 and 3) have heavy traffic both ways at both rush hours, because they begin and end in residential areas. The L trip profile is lopsided, westbound in the morning and eastbound in the evening, so the marginal gain in capacity of adding another train to it is less than to another line and the MTA is broke enough they have to make those kinds of choices.