Interesting post... I had to (unfortunately) book my next trip on the phone (thanks to the new website and the inability to book a connection leg on LX) and I won't be able to pick my seat online but a friend of mine told me the lower deck would be nicer on the A380 (quieter, less crowded since everybody wants to be "upstairs"?).
I'm thinking about calling them to change my window preferred seat to an aisle... It seems like all the window seats are already booked anyway (tried booking the second leg online and went all the way to the seat selection step). So.... upper deck, lower deck? no difference?

This is a noob's question of course