Wow, I just looked at this in detail and I have to say I'm quite disappointed.
<rant>
The X99 Micro and X99 Micro2 could run a x16 / x16 / x8 configuration with the 40-lane CPUs, but the X299 Micro is limited to at most x16 / x16 / x4. So that rules out spaced SLI since NVIDIA requires at least x8 on each card for SLI.
And why on earth would they waste space and lanes on a U.2 port is beyond me, anybody could have seen U.2 was a dead end a year ago. They should have either wired up that x4 to the bottom slot so the slots aren't a downgrade in that regard, or at least use it for a second M.2 instead and bundle or sell a M.2 to U.2 adapter for that one guy who needs it.
If you don't use U.2 (which would be most people) then there's only one M.2, so it's no improvement over the X99 Micro2. Yet to add insult to injury, the SATA situation has somehow degraded as well, dropping from 10x to 6x. Having 10 SATA ports was a bit silly anyway, but still, storage on this board makes no sense.
And the USB 3.0 header is still in that stupid location at the bottom right, so it'll interfere with mosts dual-slot video cards when installed in the second slot.
</rant>