For me personally, I prefer upper deck.

Pros:
Smaller, quieter cabin
Generally better service as a result of the above point
Side bins for extra storage

Cons:
You will need to walk all the way through the whole Economy cabin on the lower deck and then walk up the stairs at the end with your bags etc. Once you have reached your destination, it can be hit and miss, sometimes you will need to go back down the stairs and through the Economy cabin again or cabin crew will let you disembark via the upper deck once Business/First Class have disembarked.