I have the updated amd crimson drivers. it shows 16.12.2

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

Ok. When did you update? AMD launched a new 16.12.2 drivers on Jan 9, with some fixes.

Also, did the games run fine before the update? Sometimes, and I know this from personal experience, the drivers installation doesn't work as it should, and then you're better completely unninstalling them (with a tool like DDU) and reinstall them again.

so there are different 16.12.2 updates?

I believe my gpu crashed yesterday actually because I (please don't judge me i'm an idiot) tried to tinker around with the AMD wattman to slightly overclock stuff for a fix... Damn you youtube guy. we had all the same pc specs so i figured it'd be cool. 

anyway. so i uninstalled all my amd drivers and just reinstalled early this morning. so now it showed 16.12.2 and all my games stopped crashing. but no even before that since i bought this pc (august 2016) games have not run 1080p even close to 60fps. it's been disappointing. 

First question is first.
What type of Radeon 480 do you have? There is a fairly large performance delta between the vanilla 4Gb RX 480 and and say... An 8Gb RX 480 Overclocked edition from like every manufacturer.

As for your games...

1) Black Flag is a Ubisoft game. Enough said. - Disable V-Sync or download Radeon Pro and use adaptive V-Sync, turn off HBAO+/SSAO and TXAA.
The RX 480 should be more than capable of hitting and maintaining 60fps in this title. So something is up with your rig, try fixing the problem instead of throwing money away on a new GPU which might not fix the issue.

Skyrim and the Witcher are CPU heavy. Skyrim was never a well optimized game anyway and uses an abundance of scripting. - Are you running the Special Edition which uses the Fallout 4 engine?
There are mods which can increase the amount of DRAM Skyrim can use (If you aren't using the special edition), optimize the scripting etc'.

Witcher 2 is older. Disable Ubersampling, edit the configuration file to set the FPS limit at 60 and increase the render ahead count to 2.

***

With that said, Polaris, Aka. The Radeon RX 480 was never supposed to be a high-end card, people had unrealistic expectations. (Mostly because of the flops.)

It was priced and targeted as a mid-range card, so your expectations need to be aligned to match.

As for upgrading to a Geforce 1080, utterly pointless.
Your motherboard is low-end, your CPU is average... So one must assume you are only gaming at 1080P and lower anyway, so a Geforce 1080 is a waste.
You would be better served with the Geforce 1070 or upgrading the rest of your rig.

Or better yet. Upgrade none of it and get an SSD. - Using a 5400rpm must suck hardcore, how do you handle having to wait for everything to load?

No one is going to judge you for trying to improve your gaming experience, althought there are some professional reviews have a section detailing how they have overclocked the card, which can be used as another source of info.

Now, I have another question: does that pre build have enough ventilation? How many fans does it have? It's possible that the build has a reference/blower style card and, if the case doesn't have enough ventilation, it can get too hot and throttle, limiting its performance.

this is the exact pc that i bought for $650 on sale last year. for the price/performance ratio it didn't seem terrible at the time. 

Not sure if it has enough fans. but i have been checking temps; yet don't know that sweet spot it should be at for gaming. also the air mostly always is cool when i feel all around the pc.