I remember reading somewhere asking more or less the same question (the exact question was, why Acela stops at BWI but not at EWR). I think the convincing answer was that old Metroliner stopped at BWI but not at EWR, so for historical reasons Acela had a regular stop at BWI but didn't stop at EWR. Now that Amtrak/UA relationship appears dead, not sure if Acela EWR stop will ever happen.