I'm contemplating starting to sell some of the things I've been tinkering with, and I can imagine that a number of others would be interested in doing the same.
I would support instead a board with a surface mount atmega and well labeled pads connected to all of the unused pins, especially the programming pins. If you wanted to make it really hobbyist friendly, include a micro-usb connector and put the arduino bootloader on the chip. Doing this would also eliminate the huge USB-B connector, DC jack, and header pins leaving you with a completely SMD board. You most likely would be fabricating an additional board anyways (as an Arduino shield) so there is no extra cost for this approach and you can shrink your board thickness by ~0.5" (as well as the other dimensions if you don't need the extra space)
That said, if you were selling project kits to Arduino owners, it would make sense to stick with that form factor.
Arduino under the hood would make the product somewhat more attractive; I can hack it to do whatever I need it to do.