The i5-4690 is a faster chip: 3.5GHz turbo 3.9GHz compared to 3.2GHz turbo 3.6GHz. True the Skylake has an IPC advantage so its base 3.2GHz is more like a 3.3GHz Haswell, but I'd still expect the 4690 to perform better.
Evaluate the whole package here, you can't base it on the CPU price alone. Compare with an H97 board and an H110 board. If you need to buy new DDR3, then the Skylake has a good argument since the entire package will be similar in cost. If you have 8+GB of DDR3-1600+ and want to reuse that, then the 4690 has a good argument since it's a stronger CPU and costs less for you to upgrade.
EDIT: I see that you've already purchased a 2x8GB Vengence RAM kit. If it was DDR3, then you MUST buy H97 and 4690. If it was DDR4, then you MUST buy H110 and 6500. The two chips use different RAM - there's no way around this one and the decision has already been made for you if you want to use that RAM. Your other option may be to return the RAM if you decide that you want to use the other one (eg, you bought DDR3 but you want to use Skylake or you bought DDR3 and want to use Haswell).
It sounds like you want to go with the 4690 here, assuming the RAM kit is already being used in your system. It's a stronger chip and is going to cost you less overall at this point, there's not much of a reason to get Skylake in your case unless you absolutely must have an NVMe SSD.