The stations shared by NJ Transit and Amtrak are both coming in on the tunnel under the Hudson, which has limited capacity and delays both trains, though I understand that usually Amtrak gets priority. Just another headache of the Port Authority of NJ, NY, the MTA, Amtrak and whoever else fighting to get in to Penn Station.

I commute now from Albany where there's no tunnel, we are east of the Hudson the whole time and nobody to fight with to get in to Penn (except when, due to every other train having delays getting OUT of Penn there are sometimes no free tracks to come in on, but this is rare).

General rule with Amtrak in the Northeast: - Acela is pretty reliable - NE Regional and Keystone are a bit less so (Acelas seem to get priority when things are going sour) - All bets are off for everything else (i.e. anything not going from Boston to DC, or NY to Harrisburg). Amtrak doesn't own those lines, and massive delays are common.