Honestly, go with the Skylake CPU. Even if it's just an i5. My reasoning is explained in the 4th paragraph below, but in a nutshell why limit your path of upgrade? Skylake and the x170 chipset is still relatively young, and DDR4 hasn't become mainstream yet, but once driver support matures and software is programmed to utilized the increased memory bandwidth as well as features present in the x170 chipset it will eventually pay off, and cost you less in the long run when considering upgrades.
If you're like me and try to keep your computer fresh every couple of years, then eventually those costs will add up (if you go with the i7 4790K) since you will most definitely have to buy a new motherboard (with new CPU and RAM) since the i7 4790K is the tail end of practical (sub $500) consumer CPU's for the Haswell generation, and the Broadwell CPU's, well.. those were mostly 6c/8c CPU's costing $350-$999+ and mobile CPU's so your natural (most inexpensive) upgrade path if you stay with Intel is a Skylake based CPU (unless you want to wait and see how AMD's Zen CPU's perform). If you do stick with Intel, make sure to invest in a K version of the CPU, having the option to squeeze another 800-1Ghz out of the CPU to add longevity or get that extra oomph when you need it is always nice.
Honestly, I've been faced by this same question the past month or so. I recently upgraded from an old AMD PII X6 1090T w/ 8GB of DDR3-1333 and a GeForce GTX560Ti.. I was the recipient of a free R9 380 4GB card, but after a while of using it found that my CPU was bottlenecking the GPU even @ 4Ghz.
So, I browsed some of the local Fry's ads and found some killer deals and went down originally to buy an AMD FX8350/MSI 970A Krait Gaming board for $250, but remembering how when I bought my 1090T and the i7 2600K being released at that time and killing anything AMD had to offer I opted to spend $50 more for a slightly inferior MSI PC Mate H97 Board and an i5 4690.. but considering I liked to overclock I went back, spent $40 more for a Gigabyte mATX z97 board and i5 4690K ($355 after taxes). I then thought, well.. I could take the CPU back, spend $100 more and get an i7 4790K which, honestly wouldn't yield any real performance gains since I only game on this computer and forego rendering or anything that requires that kind of processor.
But none-the-less I went to Fry's yesterday originally to just rid myself of the mATX board I bought and grab the combo they had going on for $400 (after taxes) for a i7 4790 (locked) and an MSI Krait Z97 Gaming board.. but then I thought about it, for $30 more bucks I could truly future proof myself; I looked up online prices since my local Fry's will price match Newegg and Amazon and managed to spend $99 to upgrade to an MSI PC Mate z170a motherboard with quite a few features, 8GB of DDR4 3000Mhz CAS 15 RAM, and an i5 6600K and aftermarket CPU cooler (since the 6600K doesn't come with one) allowing me to possibly push the CPU to possibly 4-4.2Ghz without much issue. I originally went in for that same motherboard and RAM but just a i5 6600, but since Fry's had a promo on the board I used the difference to just get the K version.
Moral of the story is... why forego future proofing yourself? Haswell was released in 2013, it's 2016, Intel will eventually discontinue it, and motherboard makers will eventually stop producing H97/Z97 motherboards which will make finding replacement motherboards and CPU's a pain and potentially cost more since from experience I've seen retailers and private sellers put premiums on parts no longer produced in mass quantity. Look at it like this, DDR4 will most likely be mainstream by the end of 2016, early 2017. Plus with all the little features brought by the z170 chipset over the x97 chipset and considering the x170 chipset is still relatively new, most programmers/manufacturers have yet tapped into the full potential of the chipset via software so I'm sure there will be performance improvements over time once those features get fully utilized (i.e DDR4, full NVMe support etc) that just aren't present in the x97 chipsets.
Sure, performance margins might be super narrow, in some instances favoring the Haswell i7 (I'm not going to get into comparing the 4690K to the 6600K), but in the long term of things your best bet would be a Skylake CPU, even if it's just a 6600K or whatever, sure you might miss out on a few FPS difference, or 5(Zip Files)-45 seconds (3D Rendering) of time performing CPU intensive tasks,(i5 vs i7) but considering that this generation is still fresh, and at a later date you would have an option for an i7 Skylake CPU, there's just no reason (I can think of, unless you're super limited on budget, which when you're considering buying an i7 4790K that may not necessarily be the case) to forego not having a solid upgrade path for later on down the road.
The End.