It's curious, as one can make perfectly serviceable logic by connecting pull-ups to C-E's, and supplying B-E through a series resistor. So the output swings 0 to 2*Vbe or so, and the B-E is turned on and off, actively and symmetrically, with quite reasonable current. This can run down to 2V just fine, and using unbuffered outputs, supports wired-AND. I think early RTL or DTL was formatted like this, but 5V was already a standard by then.
One consideration is noise immunity. If you're wire-wrapping everything, you don't really want to have to deal with keeping ground bounce well under 1.2V. TTL's threshold band is almost 2V, which really isn't that much better.
But I suppose one should keep in mind, something hardly has to be perfect for it to become a de facto standard. Indeed, some truly awful things have become impenetrable walls of tradition. Take C programming for instance.
Another difference is TTL's input stage, which pulls up weakly. Not only does this interface with weak pull-ups and open collector signals, it's been a tradition that bus signals be idle-high, so even if left un-driven (which is normal, during arbitration on multi-master buses), signals do not accidentally become active. I don't know if PCIe does this, but even the last 2.5V PCI (and probably AGP as well?) continued in the tradition.
I believe there was also "high threshold DTL" or something like that, which is basically the thing I described, but with a 5V zener dropping input to the base (plus a B-E pulldown), so the threshold is a lot more. And the pull-ups are sized for 15V operation.
Tim