No reason other than lousy availability for Skylake, the need for fast DDR4 for optimal performance (which isn't even officially supported and may require an overclocking motherboard), and still too expensive prices.
Availability is good on all but the two higher-end unlocked parts. You are absolutely correct that Skylake carries a price premium at the low end, since the 6 or 7% performance advantage is less than the difference in price between the two low-end solutions. So if the OP asked which one was the best bang for the buck, Haswell is probably better, but that's not what he asked for anyway. The difference between the two becomes much less significant percentage-wise when we get into the midrange, though.
Skylake i5-6600 system, $393:
http://pcpartpicker.com/p/bdPWHx
Haswell i5-4690 system, $367:
http://pcpartpicker.com/p/rgkYmG
The 7% price increase in that case will net at least that much better performance, note that decent RAM is chosen for Skylake as not to make it look too cheap.
Of course, for users that will BCLK OC, the value proposition for Skylake is dramatically increased to the point where it's no contest, really.