z999z3mystorys
I'd like opinions or benchmarks if possible on how the two set-ups would compare, I know the 3dmark scores that I've seen are somewhere around 23,000 to 24,000 for 1080 SLI, and I got a score of around 21,000 points with 3 GTX 980s, so it's about a 10% increase in 3dMark.
 
the thing I don't know about, is how much games will be affected, there's vary little info on 3 way SLI benchmarks but I do know that benchmarking programs tend to scale better than games. Because of that I'm assuming the gain from 3 GTX 980s to 2 1080s will be more than 10% in most any game, but I'm trying to figure out a good way to test/measure/gather info on how much, as 10% gain wouldn't justify the upgrade.

First of all, I think 21k with 3x980 is a low score, I use 3x980 ref boards with a 5930k and get almost 28k in FireStrike.
 
I have the same doubt than yours, thinking migrating from my 3way 980gtx watercooled to 2way 1080gtx, I would prefer to stay away from SLI issues and wait for a more capable GPU as GP102, aka 1080Ti, for better single card performance, also I didn't like the "overclocking issues" within the 1080 card.
 
Very few games are optimized for 3Way SLI, you can count it on your fingers: Crysis 3, Tomb Raider 2013, Project Cars, Battlefield 4, The Witcher 3, vast majority of titles accept only 2Way SLI setups, I would recommend a powerfull single card solution for better experience.
 
The main problem is this: 3way support in games is bad, 2way setup will give you better scaling and support, single card is flawless.
 
4GB Vram, as mentioned before in the thread, is a problem too for modern games, Rise of Tomb Raider maxxed out, for example, uses more than 6GB VRAM, even a 980Ti is not enough in theory.
 
IMHO, I would skip the 1080 upgrade and go for 1080Ti single card solution in near future.
 
Cheers