The Upper Deck is preferable in my opinion as well. You don't have the inter-cabin traffic of the lower deck and it feels like you are on a private jet. Also,
they usually have additional storage bins beside the window seats, so it makes it much easier to stow and retrieve personal items during the flight without having to get up and open an overhead bin. This may be just personal experience, but I find the service is usually better up there as well (may have something to do with the flight attendant to passenger ratio being better). Try it, you'll like it!