PCIe has more uses than just the PCIe slots on the motherboard and why it may become more interesting when PCIe 4.0 doubles the pipelines available. S/ATA can use it, USB 3.0 seems to be moving from Asmedia (or other branded) dedicated controllers to the CPU and thus use it (but still connect to the the bus off cpu or not), networking is starting to use it more. I'm not sure because it was before my time, but Thunderbolt will probably use the PCIe bus as a connector the same as it did under another name. As the bus runs out of pipes needed, these standards evolve. PCI shared everything and why PCIe came around in the first place...for it's pipes.
But I don't see 4.0 being fully rolled out until next year at the earliest. Parts may start showing up, but not the whole bundle. AMD may have a first out the door since they're on the motherboard still, but Intel needs to implement this on-chip and would be slow to develop and release. Maybe Skylake/Skymont since they'll be 10nm and have room?
I just wouldn't be bothered by not having the highest number of anything. That $500 board will leave you happy for a long time very easily. That goes for the latest DX upgrade frenzy as well. DX11 has been out quite a while now and just recently have I seen playable titles really utilizing it. If you think about it, DX11 was an update for Vista and included when Windows7 rolled out. That was a long time ago in PC years, games took a while to actually utilize it, and by the time they did the cards that supported it early on were out of date themselves. Using this list
and the fact that DX11 rolled out Oct '09, it's safe to say it's fine to wait a full year to purchase a card with a new DX level. Even then, the OS needs to support it as well. Win8 is rolling out with DX11.1 and there's not much fanfare over that compared to OpenGL's progress.