I am all for eliminating the EWR stop, with a better connection all under one roof at NWK. This also makes it mentally easier for the passengers. I am not a fan of the current project because it is still not a "one-seat" ride from WTC or Jersey City to the airport. It is hard to justify extending PATH for this purpose. What you mentioned makes more sense. Bring the train right to the airport along with NJT's & Amtrak's passengers to better justify the use of a heavy rail connection.
DANGER - DO NOT GET OFF MOVING TRAIN