Just to add to that, you probably want to steer clear of the 6400 too, the baseclock is just 2.7Ghz which is pitifully low. The 6500 is only $15 more have give you 500mhz on the base clock and 300Mhz higher turbo. So I'd base your price comparison on a 6500 vs the 4460 and make your decision that way.
Otherwise I basically agree with what others have said. The performance difference isn't big, so it's really about whether the features on the newer platform are worthwhile. I'd suggest that if you're someone who just builds a rig and leaves it alone, you don't upgrade much other than the video card over time, then the Haswell build will probably serve you just fine. The big things you get from Skylake is M.2 & NVMe boot support, + (on many mobos but not all) USB 3.1 10Gbps.
I'd go Skylake personally, but I tend to upgrade and want the flexibility, is that's not you and your budget is fixed, put it into a better GPU as the previous commenter suggested.