I would sell your 2500k and then get a used 2600k/2700k on ebay to extend the life of your system until Nvidia/AMD next gen video cards comes out. I went from a 2500k 4.6 (ddr3 1600 8gb) to 3570k 4.6 (ddr3 1600 8gb) to 4690k 4.6 (ddr3 2200 16gb) to 4790k 4.8 (ddr3 2400 16gb) in the past years. The gain I received was minimal with the i5 but then HT in my current i7 helped in few games I played.
This is solid advice. The biggest issue with 2500K is lack of HT, not lack of IPC.
2600K smashes 2500K in games that use > 4 cores like TW3 or Ryse Son of Rome.
However, most modern games are still more GPU limited, and that includes TW3, Crysis 3, Ryse Son of Rome, GTA V, etc. 780 is going to hold back 2600K OC with settings maxed out in those titles.
After a swap from 2500K to 2600K/2700K, I'd start eyeing a new GPU either a GTX980 B-stock or wait for next year to get a 16nm GPU with performance roughly at 980Ti's level.
http://forums.anandtech.com/showpost.php?p=37684080&postcount=4726
In short 30-40% IPC another 5-60% fom HT and in some games more than twice performance(crysis3)
Just look at frametimes and comparable FPS.Fraps is there only for min fps.
But
you will need upgrade your gpu
Yup. Although between a move from i5 2500K -> Skylake or a 2600K/2700K swap + GPU upgrade, if on a limited budget, I'd pick the latter. Just upgrading to Skylake 6700K isn't going to solve the situation in TW3. This is one of those 2015 games that just kills every GPU out besides 980Ti/Titan X.
Only problem with this, is you are giving up a known quantity in a 2500k that overclocks well for a 2600k of unknown history, or at least you have to trust the seller. If buying new, yes, hyperthreading is worth 40.00, and probably even the extra hundred dollars it costs you new. But to go used, especially giving up a good chip, is a bit risky.
There isn't much risk really because almost all SB chips hit 4.4-4.5Ghz on stock voltage. That was one of the biggest advantages of SB over IVB and Haswell. To not get 4.4Ghz on a 2600K would be highly unlikely especially if overvolting.
I know the cpu itself will give me about 15-20% but will I see an increase with the motherboard as well as its newer, pcie 3.0 etc.
Thoughts?
With your GPU, almost none. With a 980 the difference is only 2% between PCIe 2.0 x16 and PCIe 3.0 x16.
The Witcher 3 is just one of those crazy demanding games that hammers older GPUs like 780. Even with a 5960X @ 4.4Ghz, you will be lucky to get 40 fps average in demanding scenes at 1080P.