I traced a DC to Boston route, going MARC-SEPTA-NJ Transit-Metro North-Shore Line East-MBTA. The entire route along the NEC, all stops, using current schedules and doing some logical extensions... was nearly 16 hours, and no cafe. Oh, and transfers at Newark/Wilmington, Philadelphia, Trenton, Penn Station/Grand Central (Yes, you gotta take two subway lines between the two), New Haven, and Providence.

Compare with the Amtrak Regional which was 8 hours with a cafe. Set aside the expensive Acela.

Cheap? Sure, I'll give you that. But you got multiple transfers, one requiring a "complicated" path because of how the two train stations are. Your timing's going to be tight, and you may be able to grab lunch somewhere, but you're be ready for dinner at Boston South Station and you've spent all day.

Lets throw in airlines, Dec 4 for example. Southwest, BWI to Boston Logan. 1.5 hours flight time, 2 hours buffer at BWI, 30 min to get whatever luggage (remember, 2 bags fly free). That's 4 hours... for $50 flat one way. Amtrak? $132, 8 hours, one way... but then you miss getting scanned, frisked, and repeated sniffed in the butt by a TSA K-9 unit. (I won't go into sarcastic details there)

The point here is there's an overall quality of service. Sure, you'll get there with end-to-end commuter rail. But if your timing sucks... it'll be a hell ride.