AA is unlikely to do anything for you beyond rebook you on the next AA/US flights. Unless the misconnect is due to MX, you're unlikely to have your hotel and food covered.

The microhops such as EWR-PHL are the first flights to be cancelled/delayed the second ATC issues arise in the northeast. I am surprised that the stats are as good as they are for your flight.

Why not simply book EWR-BOS on UA or take Amtrak. Lots of nonstop flights and the Acela is pleasant, if a bit longer (although not so sure with the routing you propose).