Having 28 PCIe 3.0 lanes means dual GPU setups are at PCIe 3.0 x16/x8 (rather than x16/x16), and tri-GPU setups are at x8/x8/x8 (rather than x16/x16/x8). Very few PC games lose out due to having PCIe 3.0 x8 over PCIe 3.0 x16, meaning that performance should be almost identical. On paper, there should be a smaller performance difference with this setup than if the frequency had been reduced, or the fact that people would complain if there were fewer cores. Having six cores puts it above the i7-4790K in terms of market position and pricing, and the overall loss is that an i7-5820K user cannot use 4-way SLI, which is a very small minority to begin with.
The only downside to all the 28 PCIe 3.0 lanes is that there is no physical way to improve the PCIe lane situation. If the frequency was low, the user could overclock. If there were fewer cores, overclocking would also help mitigate that. Despite this, on paper it looks like that performance difference should be minimal.