Here's my take on this...
Go with what works.
This is the interior of the Bi-level Alstom (TGV) Duplex which will fit into NYP and appears to have a fairly roomy design, with fold down luggage racks as well as ample other luggage space due to its articulated design.
It would make sense for Amtrak to order these sets at the same time California orders their sets. Here are a few color schemes, one for the NEC and one for CAL.
I've gone ahead and modeled the NEC version in miniature here:
http://youtu.be/6IgZyLyRw34
Current capacity can be done with single level, sure. But there will come a time maybe 10 or 20 years from now when this makes more sense. And Amtrak can outfit these things however they like and make them as roomy as needed for each class of service.
My 2 cents.