A few observations/opinions:
Full-sized ATX for Z97 is overkill (unless you have a boatload of non-GPU add-in cards). The sweet spot for Z97 should be uATX. Z97 can do SLI or XFire on a uATX board. If one wants or needs triple or quad GPU horsepower, you should really move on up to X-series chipsets where full-ATX or larger makes more sense.
Onboard wifi (and/or Bluetooth) may be convenient, but it's not doing anything that a dongle can't do and is generally NOT upgradeable when wifi standards inevitably change. Plus, some implementations may not provide flexibility in the placement of antennas for optimal signal strength. As uATX will address the add-in card needs of the majority of gamers (1 dual-slot GPU + 2 miscellaneous add-ins), then onboard wifi is a waste of precious board area better used to implement other features pertinent to the board form factor and target audience such as improved audio or cutting-edge device support.
Thunderbolt is very unlikely to make inroads on non-Apple PCs at this point, so I can't understand why the manufacturers keep including the headers for it, unless they somehow are contractually obligated to do so.
Can we just agree that enthusiasts (who the Z97 chipset is targeted at) will have at least one discrete GPU, so providing lots of display connectivity options in the board IO area is (again) likely wasted space and materials that will infrequently (at best) be used. Manufacturers should be sparing in their use of such parts on enthusiast-oriented boards.