Goes back to the ISA/PCI days. ISA cards faced "up" in towers or right in desktop cases. PCI came along and someone noticed they could fit the ISA and PCI slots in such a way as to share one of the case openings, thus offering "4 ISA 4 PCI, 1 Shared" motherboards that worked with normal 7 slot cases.
And so now you know why PCI cards are upside down.
AGP - just replaced the top PCI slot. When AGP cards came out they were like the PCI of the day - no ram sinks, small heatsinks, didn't prevent use of the 1st PCI slot. Also, didn't run all that hot so cooling wasn't a concern. Should it have been? YES. I agree with those asking now and there were certainly people designing cards who knew in a couple years it'd be better to have stuff on top. But for that generation of cards there was no reason to and so they were built upside down as well.
And still are.
So why can't they flip them over now?
Because motherboard manufacturers don't allow room. You might have wondered why I was talking about first generation AGP cards above, well, this is why. Not that the cards then needed to be different, but leaving room above the card on the motherboard needed to be made an AGP spec at the time. It's not. Still isn't. So while your board of the moment may have enough room, your friend's board might have a capacitor sticking out that would contact with a heatsink and prevent installation. Or one card might fit in yours and another wouldn't. On some micro boards they might even run into the cpu hs/f or ram, point is, there's no room reserved for up top parts, and though some cards do offer backside ram now you might notice even some of those don't put ramsinks on the back chips.
What's the solution? Get it as part of the spec. Not bloody likely now. Want your cards facing the right way you better get on the case of the PCI-Express people to make sure they are.
Or turn your computer over.
btw, asked this back in
June
--Mc