Technical support calls, lots of them. People shove a 2x card into a 4x slot and find out either it doesn't work or it isn't getting the bandwidth they expected.
Most hardware isn't set up to handle it because it isn't in the PCI-SIG specifications. Even by the off chance that some motherboards are wired for 2x, that doesn't mean the BIOS are ready.
We are against it because there's a high likelihood that if you buy a 2x card, either the system BIOS is going to reject it or you're only going to end up with 1x performance. In both cases, it defeats the purpose (just buy a 4x card and a non-POS motherboard and be done with it).
It's pretty obvious PCI-SIG felt that increments smaller than 4x were unnecssary; there's no reason for that to change today. We're talking like 3/4 inch longer on the slot and 4 times the performance. The difference in size is moot because virtually all motherboards are designed for at least one 16x slot.
If they were getting rid of everything larger than 4x, for example, then I could see justification for a 2x card. That simply isn't going to happen though (at least not any time soon).