<font face="Verdana, Arial, Helvetica, sans-serif" size="2">The reason I think it's usually not allowed is because LGA/JFK has different fares than EWR to begin with with EWR usually being cheaper.</font>
These days it is typically the reverse due to America West and Jet Blue competition from JFK. Not as much transcon direct competition at EWR.
With such ridiulous fare differences between the terminals due to LCC competition, it makes no sense to treat them as co-terminals. I would love to buy ex-JFK fares and fly in and out of EWR.