PC's originally used desktop cases and the expansion cards sat vertically. The is structurally sounder, and actually provides better cooling . When the first towers appeared ISA was still in use and indeed the components were usually on the top of the cards when mounted horizontally. With the advent of PCI and the mixing of the slots on the motherboard, the components moved to the other side of the cards. In a tower case this puts them on the bottom and the situation ahs remained this way ever since as the spacing of the card slots via the rear bracket would need to be changed in order to move the component area to the top and there is just too much inertia from the hardware base currently installed to make it viable.
The BTX tried it as noted with very limited success. The Silverstone TJ03 (I think) also tried to invert the card positions but didn't go over too well. Some of the newer "top mount" cases are another variation (and not a newone as Northgate did that with their full tower in the 90's).
It would really take a combined effort of motherboard, expansion board and case manufacturers to collaborate on some new models if they wanted to move away from the current layout.
Frankly, I'd love a full sized desktop case again. I tried to find one of the convertible (tower to desktop) cooler masters when I built this machine, but they were nowhere to be found.