Hi John
I get your point but ....
I don't have an electronics background so when I hear SPI I go Whaaaat?

Connect to serial port??? how???

With the shields supported with libraries I can easily get going. I have done some successful projects already. I guess that the shields are one of the things Arduino is popular for.
So I guess fixing the pin incompatibility problem is a good thing for Arduino. I'm pretty sure that it can be done with a double sided PCB with (at least 1, worst case 3) extra row(s) (or however this is called). I have however never designed a PCB, take away a double sided one which in my humble opinion I think is needed. When I read comments on board designs I don't feel comfortable about starting it :~
I also have another reason why I prefer the shields to loosely connected boards. That is the fact that the shields cause a mechanical resistant towards movement between the boards, which makes assembling the electronics in a mobile device easier than a bunch of boards connected with wires.
I have taken the liberty of using ladyada's pcb to show what I'm thinking of.

Does something like this exist? Is it possible? Someone interested in designing this?
Best regards
Jantje