I definitely prefer the upper deck if flying business class. Much quieter and better service from the FAs I think. I have never noticed any issue with cieling height, it is not like you have to duck down or anything. The only drawback is it takes a bit longer to deplane from the upper deck.

I actually wish more arielines had 1st on the upper deck of the 747, I just really like sitting up there. It is a cool sensation at takeoff to be sitting in a small cabin with the 747 roaring off the runway below you.