They are pretty similar as everyone here has already noted. The only other differences I can immediately tell is that the pcb and controler are slightly different and moved around a bit. Some of this has to do with the Dual USB and some probably has to do with maybe better/smaller tech.
Ooops! I almost forgot, the older HHKB Pro 1 has slightly thicker and heavier keycaps compared to the HHKB Pro2. I think it was only like 2 tenths of a gram more though. I don't know if that was a long lasting or consistent trend though. And it certainly does not make a noticable difference.
I dig imav's 50/50 cookie board too =)