It probably wouldn't hurt to wait for Skylake, since it's the first of the future DDR4 line. Though I don't think it's absolutely necessary, and it usually takes a generation or two before you start seeing vast performance differences among RAM generations. Plus, you probably will be spending more than $2000 to upgrade to it. I'll leave this entirely to your discretion, since I'm currently of the opinion that getting a solid current generation CPU will do you about as well as waiting for the latest and greatest coming out at the end of the year.
As far as the APIs go, any DX11 card will support DX12 out of the box, and I assume the same applies to Mantle. The current generation of cards are already pretty well future proofed.
If you were going with Intel, I'd just say get a good i5 Broadwell chip, a mid-high end GPU, and be done with it. Provided you're not absolutely obsessive about playing all your games at absolute max settings, it'd last you about 4-5 years. Going AMD will probably give you about as much lasting power for games, but since I don't keep up with that scene, I'll defer to Bradl or Lowend for their opinion on that.