Got my Micro 2 2 weeks ago... an awesome board..
Concerning the USB 3 Header:
Imagine a vertical alignment of the Mainboard, as in my case with the Aerocool DS Cube..
An USB 3 header facing down (as in the prototype versions) would render such a build impossible..
So I can see why EVGA moved back to the 'ordinary' header.
But then again, why not placing the header anywhere else, where it never would interfere with anything else..
The second issue is far more severe for me:
I can't get the M.2 AND the PCIe Slot 3 get to work at the same time..
the problem is manifold:
* Using the Samsung 950 Pro in M.2 slot
* I have the right processor: 5930K (28 lanes 5820K vs. the better 5930K and 5960X with 40 lanes)
* The manual from EVGA states, that it should work with 40 lanes, though, reducing PCIe Slot 3 from x8 to x4, which is fine for me, I need it for a lane-wise 'cheap' expansion, ASRock USB3.1. TypeA/C card, using x2 lanes only
* The BIOS (v. 1.02, current) states that by enabling M.2 slot, the PCIe Slot 3 is disabled, and it indeed is greyed out in the BIOS
* Asking EVGA about the issue: --> "It should work"
* Reading the Review here on SFF: "Edit: After further testing, the BIOS option description is incorrect and it actually is shared like the manual says. So with a 40-lane CPU the bottom PCIe slot will be reduced to 3.0 x4 when the M.2 slot is enabled, the bottom slot will still be disabled with the 5820K when the M.2 is turned on."
* Reading the EVGA forum: "To your first question with a 40 Lane CPU, you will have PE1 @ x16, PE2 x16 for both GPUs and a choice to have either a Wifi Card or a M.2 PCI-E SSD. You can't have both as the M.2 disables the PE3 slot."
*** Testing it myself: (5930K, Gigabyte 970 GTX Gaming G1, EVGA 750 Ti FTW, ASRock 3.1 USB Card, Samsung 950 Pro 512 GB)
==> With M.2 enabled: Samsung 950 Pro works, ASRock USB 3.1 card does NOT work
==> With M.2 disabled: Samsung 950 Pro does not work (obviously), ASRock USB 3.1 DOES work (showing up as x2 Gen 2)
So I can't get the sense behind all this, how could you guys from SFF Review of the Micro 2, conclude, that it works? Even after further testing... 
Did I do something wrong in the setup?
I'd really appreciate any help on that issue, cause I was considering every detail meticulously, when setting up my new rig..
PS: The 750 Ti FTW will have a water cooling to bring it down to 1 slot in use, to fit all 3 cards in the built, but this is another issue of its own..
