Septa is a reasonable option if you're only taking one train. A sample commute for the OP is the R2 leaving Wilmington at 7:08 and arriving at 30th street at 7:47 then taking the R3 from 30th street at 8:12 and arriving in Trenton at 9:18. That's a horrible commute and that's just one way. Switching over to NJ Transit in 30th street doesn't improve things much and only adds to the cost. (Edited to add: I see the OP is going the other way in the morning but it doesn't really make any difference)

But you're right, Amtrak isn't a commuter rail service.