Yeah, the Xeon-E3 lines lack of PCI-e lanes is really underwhelming. I've got a LSI 9200-8e and Mellanox Connect-X 2 in my ProLiant ML10 used as my FreeNAS box, leaving a total of 4 PCIe lanes available - thankfully I don't see any need for more AIB's in this machine, but if I used it as a workstation that needed a GPU + another board or two it'd be a really awful situation to be in.

Considering how hard Intel is pushing Thunderbolt it makes little sense how hard they're gimping their consumer and workstation CPU's when it comes to PCIe support.