Thoughts on my first mini pc build?

It is a really good build.

nevermind

Case:

1 x Corsair Graphite 380T w/ Side Window Panel [Black] [Alternate Colors Available] $99.00
10092
Chassis Options

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I meant what motherboard and why that psu? That case will hold a regular ATX psu.

Should be working fine.

Go for a dedicated SSD with quality, don't know what you mean by putting a no name 250GB listing.
Get the Samsung 850 Evo 250GB. Good performance drive which is the best value SSD on the market.
Goes for about $90 last I checked.
Not much point getting a Hybrid drive at 5400RPM, stick to 7200RPM if you can, much better performance.
Is this build for gaming, and what is your budget?
Also any reason you've gone for the 6900x? What are you purposes?
Don't go for the MSI Armor 1080, it is a budget oriented model, which has worse cooling than the Gaming line.
Get the Gaming X, which has better cooling and a factory overclock.

Budget is currently around 4 grand. Went with the 6900 just because lol.

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Kingmanbc, you realize you are going to pay $4000 for a $2000 PC? Do not buy a 6900 "just because". Save yourself a $1000 by getting an i7 6700k + z170 motherboard. Also, get a better psu.

It's not a bad psu, you're just paying more because it's little, but you don't need a psu that small. You could have bought a better psu for half the price.

Geez it sounds like I need to go get a job working for xotic

Yep....
Annoys me when reputable stores have people who give garbage quotes, and suggest you buy certain parts because they'll make a higher profit margin off it. Can't trust em...

I've got a build together and gone with a red and black color scheme for now, let me know if you have any preferences in this regard, or any cases you've had your eye on.
I've also gone for the EVGA GQ 1000w simply due to it's amazing value and high quality, going $20 off at the moment, beating out most good modular 850w power supplies, with the exception of the M12II which is $5 less.
If you want, I can get an EVGA G2 power supply which is a little more expensive , but this means I can fit it with custom cables to add to your build.
I'll post an example of this in a second build.
Given the EVGA graphics cards an estimate price as well.
I've left in some high end RAM selections for you to choose from that fit a white and black color scheme, but then again, once you let me know what color your want your build to be I can change these out of need be.
ATX PC:
PCPartPicker part list: http://pcpartpicker.com/list/yvDDxY
Price breakdown by merchant: http://pcpartpicker.com/list/yvDDxY/by_merchant/

CPU: Intel Core i7-5820K 3.3GHz 6-Core Processor ($369.99 @ SuperBiiz)
CPU Cooler: Noctua NH-D15 82.5 CFM CPU Cooler ($88.33 @ OutletPC)
Motherboard: Asus X99-A II ATX LGA2011-3 Motherboard ($225.99 @ SuperBiiz)
Memory: Corsair Dominator Platinum 32GB (2 x 16GB) DDR4-3000 Memory (Purchased For $0.00)
Memory: Corsair Vengeance LED 32GB (2 x 16GB) DDR4-3000 Memory ($189.99 @ Newegg)
Storage: Samsung 850 EVO-Series 250GB 2.5" Solid State Drive ($89.99 @ Newegg)
Storage: Western Digital BLACK SERIES 2TB 3.5" 7200RPM Internal Hard Drive ($119.99 @ SuperBiiz)
Video Card: EVGA GeForce GTX 1080 8GB FTW Gaming ACX 3.0 Video Card (2-Way SLI) ($700.00)
Video Card: EVGA GeForce GTX 1080 8GB FTW Gaming ACX 3.0 Video Card (2-Way SLI) ($700.00)
Case: Phanteks Enthoo Evolv ATX Glass ATX Mid Tower Case ($200.43 @ Amazon)
Power Supply: EVGA 1000W 80+ Gold Certified Semi-Modular ATX Power Supply ($109.99 @ Newegg)
Operating System: Microsoft Windows 10 Home OEM 64-bit ($88.89 @ OutletPC)
Total: $2883.59
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2016-08-06 12:02 EDT-0400

@OP do you want SLI?
Because you can get a hell of a lot more performance out of your PC, and use two 1080s.

Make sure you get your money back

You can't run SLI in an ITX build, and given your budget I'd assume you want the most performance possible.
Are you okay with only a single card build? Because that's the sacrifice you're going to have to make with ITX.

1080 ultra at 1080p yes. But spending some extra oney on a mobo that can run SLI is not a bad idea imo. 50$ more?

Yes. 4K @ 30fps but 60fps is a whole new experience