Your CPU is a huge bottleneck for GTX1080 at 1080p. The most you should buy is a GTX1070. Future proofing with a 1080 is a waste of time and money. You picked the worst time to buy a 1080 since NV is rumored to be launching 1080Ti around March 10th (PAX East). Sell the RX480 and get the cheapest open-air cooled (no blower) GTX1070. Later on, sell your processor and buy a used 6700K/7700K and then upgrade to Volta in 2018-2019. GTX1080 is also way overpriced for what you get. It's only 20-24% faster than the $380 1070. Not worth the $ unless you have top of the line CPU like 6700K @ 4.5Ghz:

https://www.techpowerup.com/reviews/ASUS/GTX_1050_Ti_Strix_OC/29.html

Honestly, your processor will even bottleneck the GTX1070. Modern games use 4-8 threads and your only have an i5. On top of that, when all 4 cores are loaded, your CPU only runs at 2.7Ghz!

https://ark.intel.com/m/products/88185/Intel-Core-i5-6400-Processor-6M-Cache-up-to-3_30-GHz#@product/specifications

New 7700K hits 5-5.2Ghz:

https://www.techpowerup.com/229667/msi-z270-motherboards-automate-core-i7-7700k-overclock-to-5-20-ghz

RX480 is not the only weak point of your system. You also aren't aware that some games you mentioned are unoptimized turds. Like turning on MSAA and HairWorks in the Witcher 3 will wipe the floor with your card. 

Black Flag, as all modern Assassin's Creed games, is an unotimized pile of Anvil Next engine garbage. At 1080p, 780Ti and 290X drop to 43-44 fps with SMAA and to 35-39 fps with MSAA:

http://gamegpu.com/action-/-fps-/-tps/assassin-s-creed-4-black-flag-test-gpu.html

Your CPU is not fast enough to maintain 60 fps in Black Flag either (see CPU charts from the same link above). 

You would be 10x better off building an 8-core Zen or 7700K/6800K overclocked system after reselling your mobo/CPU and getting a 1070 with the $ saved from buying a 1080. You would have a well-balanced system. If you buy a GTX1080, in 2 years that card is worth $300 max and you have a slow CPU platform. You are stuck on what to do. With my approach, you just sell the 1070 and get a new Volta x70 series card for $380-400. 2017 is a good year with Zen, Kaby Lake and the new X299 Skylake-X platform. Lots of great choices. 

Around May-June AMD should release Vega and we may see Pascal 1170/1180 refreshes. Spending $550-600 on a 7+ months old 1080 is money wasted given your system's specs. 

You are also memory bandwidth bottlenecked. DDR4-2400 isn't fast enough for Skylake. DDR4-3000 is minimum to alleviate the bottleneck of 6700K/7600K/7700K. In your case it doesn't matter since your CPU is slow but should you upgrade to faster CPUs, that RAM bottleneck will show up at 1080p when using a GPU as powerful as the 1080:

https://youtu.be/gYb0y8LNAVI

Hope you learned some things today :) 

Your cheapest move is to sell the 480 and get a 1070. You can do the CPU/platform upgrade in the 2nd half of 2017.

You don't need to waste your money over GTX 1080, there's no "future proof" such thing, you going to be forced lowering down to low-med graphics setting in 2 years overtime, so don't do it, a lot of GTX 780/980 owners found it wasted, and upgraded to GTX 1060/1070 least and then lowered few graphics setting a bit.

Also, your RX 480 should be fine at 1080p, you need to tweak/optimize in-game graphics setting and always update driver to get the games run smoothly & stable(or sometime could be gets worse xD), that is why Nvidia decided to make their own optimization guide in site and Geforce experience app for Nvidia owners.

You need an SSD for Windows and programs, running everything on a 5400 rpm HDD is a bad joke.

AMD 480 is more than enough for 1080p and 60+ fps in all games but the badly optimized ones at release.

For the first time in history we live in a time when a 200 usd video card plays all games at ultra at 1080p at 60+ fps.

Ok so there are severa versions of the GTX 1080 some have the reference design and are slower while others are oced and have a better cooler.

Zotac AMP Extreme is for example one of the fastest 1080. However there are two versions one with 2 fans and one with 3 fans the extreme version is with the 3 fans and is the faster version.

Do not take any Founders Edition Cards they are overpriced and slow.

The most important question is, what monitor do you have, which resolutions are you trying to achieve?

As others pointed out, if you buy a gtx 1080, that CPU will bottleneck you like crazy. I would suggest the following, unless you're really hurting for a new machine, give it a few months and see what AMD comes up with both on the CPU and GPUs (Ryzen and Vega).

The rumors are pretty strong that the IPC improvements will make them the better choice against the latest from Nvidia and Intel. Especially on a price/performance analysis.

Also, there's no such thing as future proofing a PC. You should always buy the most balanced machine you can afford for the display that you want to use.

Are you sure they didn't sell you this "RX" 480 graphic card? ;)

Then there is something wrong with your system. My girlfriend rocks an RX 480 and that thing runs The Wicther III at Ultra settings 1080p (without hairworks) at 45-70fps.

The scores of your games are way off, the RX 480 should be a very capable 1080p/1440p card.

His CPU is a huge bottleneck? Even an ancient i5-2500K (not overclocked) is more than enough in most (not all) games:

Yeah, I have a 4th gen Core I5 (4670k)and it does just well.

I have a SLI of two GTX 980 and can do 5760 x 1080p in medium to high @45 fps... EDIT: @45 fps in the Witcher 3.

I have the updated amd crimson drivers. it shows 16.12.2