House Question #1 -Floor vs. Ceiling

I'm going to field a bunch of questions here probably because I need some input. Our first HUGE house project is replacing the radiant heat with a new forced air furnace and A/C. Obviously running ductwork is going to be interesting. One thing I'm wondering since I have the choice. Should we install the vents in the floor or the ceiling. In the upstairs there is no question we'll be putting it through the ceiling. However, in the downstairs it wouldn't be much of a pain to do it either way.

I think all new houses do the floor.... is that right? I assume it's an efficiency thing but if there is an argument for ceiling vents I think I might lean that way to avoid cutting holes in the floor and the limitations on furniture placement, etc.