I've heard 6th gen i7 is not good for deep learning because its PCIe performance is crippled (16 PCIe lanes instead of 40 in previous generations, it should matter for dual GPU use case). Don't quote me on that ;) Used xeons 2670v1 are dirt cheap on ebay now, and they are modern enough. Single-core performance is worse than in modern desktop CPUs, but not too much, multi-core performance is great, and these xeons allow to install lots of RAM.
If you don't want that much RAM then for the same price a single desktop CPU (i7 5th gen?) could work better because of a higher clock rate.
[1] http://www.techspot.com/review/1155-affordable-dual-xeon-pc/
Usually pcpartpicker builds have comments, did you not submit your build for review? (I don't actually know how the site works).
ASRock EP2C602-2T/D16 has EEB 12" x 13" form factor, it may be a bit harder to find a case for it (but that's possible, at least form factor is standard). Also, it has 2 PCIe slots which means you can insert only a single GPU - each GPU usually takes 2 nearby slots. Nice thing is that you can put more RAM sticks; it means you can either get more RAM or save money by using e.g. 8GB sticks instead of 16GB sticks which are cheaper per GB.
There are Supermicro motherboards similar to ASUS Z9PA-D8C, but AFAIK they have non-standard mounting points, and Supermicro branded cases are very pricely. There is also a few other ASUS motherboards (Z9PE-D8 WS, Z9PE-D16); they have nice features - D16 has more RAM slots and D8 WS has more PCIe slots, but D8 WS cost more and they both don't use ATX form factor (though their form factor is still standard).
The motherboard I've chosen is not without gotchas - CPU slots are very close to each other, so you can't use a cooler which exceeds CPU slot size; most popular coolers don't fit. To install Ubuntu I had to first use integrated video to install nvidia drivers, and then I had to disable the integrated video using an on-board jumper (there were some Ubuntu configuration problems with both internal and nvidia gpus active), but likely this is not specific to this MB.
There may be other motherboards; look for C602 chipset, check what's the form factor, how many RAM and PCIe 16x slots are there, how is PCIe speed adjusted when several slots are occupied (e.g. often 16x slot can become 8x slot when something is inserted in another slot), and check MB image to understand how are PCIe slots layed out: when two of them are next to each other a GPU covers them both. E.g. ASRock Rack EP2C602 looks fine (it is EEB, and no USB3, but CPU slots are layed out better than in ASUS Z9PA-D8C, you can use more cooler models, and it is a bit cheaper). No idea about which brands are better, I only built such computer once.