Only the mightiest of today's newer graphic cards - 12GB Titan X, workstation cards, etc - can fully saturate x16 PCIe 2.0 bandwidth and thus gain any real benefit from PCIe 3.0. A multi-GPU through x8/x8 PCIe 2.0 usually splits bandwidth evenly enough that PCIe 3.0 still isn't a substantial upgrade - at least so long as a direct electrical GPU bridge is used instead of "bridgeless" links across the PCIe bus. 3-way multi-GPU under load can be throttled by x8/x4/x4 PCIe 2.0 in some games (it depends a lot on how they use GPU resources). Benchmarks can demonstrate the limits, but they don't always represent actual real-world performance. Many games are better optimized for AMD or for NVidia, some games will run noticeably better on one platform than on the other (and I think this is an important point when deciding on a platform meant to run some particular game you might have your heart set on.)
Some oddities have been noted where particular games run faster on PCIe 2.0 than PCIe 3.0, or run faster without HyperThreading, or whatever. Just quirky hardware/software combinations which seem to run unexpectedly well or unexpectedly awful together.
AMD motherboards rarely support SLI, it's an NVidia licensing thing. An AMD FX9590/RV990FX/SB950/DDR3 or an AMD A10-7870K/A88X/DDR3 platform running 2-GPU CrossFire can still impressive enough for "elite" gamers - and have a lower overall price tag.
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