Without a doubt, upper deck is much quieter than the lower deck. I've been on 8 CX flights in the past 3 months and consistent found that upper deck offered a more peaceful environment.

In addition, with two seats on each side the cabin is cozier. You also have plenty of storage space on the overhead, on the side storage boxes, and the stowage behind the stairs for wheeled carry-ons.

There are usually 2 lavatories, and they are almost always vacant when you need to use them. I cannot say the same for the lower deck, as they are sometimes used by Y class passengers forcing J/C class passengers to wait for lavatories.

However, it has also been my experience that the upper deck has higher temperature than the lower deck. But then again, I've been literally "freezing" in the F cabin on the same aircraft.