The only real difference is that your sketch communicating on serial will probably have to take into account the faster (115800) baud rate that the 8U2 operates at.
Relax people it COULD be used for evil, but so COULD a FTDI chip, it has the same lockout capability if you wanted to use it.
The only problem this new feature set presents is a very slight annoyance in that there is a bootloader fork.
The Arduino team were right going this route, but it means UNO compatible 328 bootloader (optiboot) chips and Duemilanove compatible bootloader chips will not work interchangably in UNO and Duemilanove boards (with out chip re loading).
My first reaction when I heard the hardware specs were some of the same cynicism, I was jumping to "oh well they have a right to make some money and close it" but the second I heard that the loader on the 8U2 is LUFA http://www.fourwalledcubicle.com/LUFA.php
I went "WOOHOO OPEN SOURCE LIVES"
Relax and wait for more info, I guarantee you its the same Arduino you have come to rely on, with a little more mainstream (non hobby) street cred.
The Arduino just got a hair cut and hid the tats, but it's still not the man, MAN.
BOZ