I'd say it depends on the cpu. The Asus A II is newer and supports the new 14nm cpus such as the i7 6800k. The older Asus A 3.1 supports 22nm cpus such as the i7-5820k. Whether this is changed due to bios updates etc I dunno.
What I do know is that while those x99 boards are fully optioned, nobody uses most of them. My z77 has TPU, EPU, mem-ok switches, also in bios. None get used. One is for software OC, one is Eco settings (on a overclocking board?).
So choose the board that DOES have the options you WILL use, looks acceptable or better, fits what you need it to do. Worrying over which board had or didn't have useless or undesirable options is pointless.