Turn off Wake-on-LAN in the network interface driver -- That's been known to cause problems.
Unless you're running RAID, there's no need to use the Intel Rapid Storage driver/software and you're better off without it. I do, however, use the Intel SATA chipset driver still.
I run with both fast boot and hibernation disabled, and the hibernation file completely deleted so that Windows has no choice but to either suspend to RAM or completely shut down. The computer has to dual-boot a second installation of WIndows 10, anyway, so it's a bit safer for multi-boot Windows that way anyhow.
If you have a spare drive, try a bare-bones Windows install with just the minimal drivers and no AI Suite / Wake-on-LAN / Intel Rapid Storage. You can probably leave Fast Boot and hibernation on, although it's usually best on desktops to turn it off. Fast Boot still uses the hibernation file. Test for stability in a minimal configuration. If it works OK that way and can sleep/wake/shutdown without problems, then the board probably isn't the problem.
This isn't necessarily an ASUS or AI Suite problem -- other manufacturers have had similar problems with utilities that communicate with lower-level BIOS functions on Skylake platforms. It may be at least partially an Intel problem, combined with subtle changes in Windows. (Gotta love undocumented Windows patches and changes...)
Motherboard: Maximus VIII Hero
Processor: I7 6700K - 4.9GHz OC
CPU Cooler: Corsair H80i v2
Memory: G.Skill DDR4-3000 16GB
Graphics: EVGA GTX 1080 FTW2 1721/1860MHz
Storage #1: 1TB Western Digital Black
Storage #2: 2TB Western Digital Black
Case: Antec Nine Hundred
Power Supply: Antec Edge 650 80+ Gold
OS: Windows 10 Pro