Seems to me that the disappearance of EWR as a coterminal for JFK/LGA happened a while ago (at least a couple months, and maybe three or four months or more). I don't often fly in/out of LGA/EWR anymore, but I have noticed it in the fare rules on the few tickets that I have bought.
I agree that it's too bad, and I'm not sure what benefit UA gets from it. Obviously, if they wanted to match anther carrier on a particular route, they could make that fare ineligible for coterminal standby. But in this case, it seems to me that EWR (and BWI I gather) just disappeared from the usual laundry list of coterminals. Maybe too many people were taking advantage of the option and UA couldn't predict loads well enough anymore.
BTW -- why do you suppose UA lists CGX/MDW/ORD/CHI as coterminals? After all, CGX doesn't exist any more and UA doesn't fly to MDW (and hasn't in a long time, if ever).