Depends on a bunch of things, as at ITX level the board layout can become critically important. Which case you are using can become a significant factor.
If you were comparing a larger form factor though, and basically just weighing up the differences between H97 and Z97 then it's almost exclusively down to two things - CPU overclocking and the ability to split PCIe lanes (enabling the use of XFire/SLI).
The only caveat to that is that while the chipsets are near to identical, the motherboards they are appear on are less so. As H97 represents a more mainstream option, they will sometimes remove/not support features which are part of the chipset specs, the most obvious example being M.2. Of the 24 H97 motherboards currently on sale (US PCpartpicker) only 11 of those have an M.2 slot.
At ITX level, Z97 makes zero sense if you aren't overclocking, however if you require something that only a Z97 board can provide, or a layout which suits your case better, the price difference can seem much less significant.