The Asrock Z87 boards, and the lower end Asus boards have PCI for those who need it. It's probably made available with a PCIe to PCI bridging chip, which will no doubt add a little bit of latency, and maybe pinch a PCIe lane.
Regarding the USB3 bug, I've already tested the USB3 devices that I will be using on a Z87 board, and they all seem fine.
I've pretty much decided on a 4770K, but haven't made up my mind about a motherboard yet.
Three that catch my eye is the Asus Z87 Sabertooth ,Asus Z87 -Expert, and the Z87 Pro.
The Asus Z87 Deluxe/Dual looks awesome with its twin Thunderbolt ports, but isn't available yet, so no price. But I bet its pretty expensive.