I actually picked up an Ls3 from an 11 Corvette about a month ago.

While the LS3 is a better engine, the combo you have with the LS2 and auto is already "mated", saving much time and money and tune (money) with prematched components. There are a lot of "year" specific with these auto vs manual and this ls vs that ls, so if you want simplicity (depending on your skill level (time) and less cost ($$) then i'd go with the combo.

My opinion however (ask me how i know lol)

Mike