ASUS N56JR (i7-4700HQ, FullHD GTX760M) with Samsung 840 Pro 256GB SSD and 16GB RAM, bought a few days ago, almost all useless softwares and apps removed and nothing installed yet except for skype desktop version. No swap, energy saving options set to max performance and fast boot option disabled. Local account login and no Microsoft account automatic connection allowed.
With Windows 8 Pro everything was fine, updated to 8.1 and boot took a few seconds more (so nothing important) but shutdown became minutes. Absolutely unexceptable.
After two days of attempts, including the suggested Clean Boot and similar, which was useless and made me install unwanted software, I tried the suggested solution of disabling one-by-one all the drivers. Finally it worked simply switching off the Bluetooth module (Qualcomm Atheros). Now everything seems to work, and these are my times: shutdown in less than 4 seconds, login screen in 11 seconds (from completely switched off computer), desktop in 15 seconds and complete boot in 24 seconds.
A little off topic: it seems that the Intel Graphics driver (10.18.10.3308) it's not working fine since the writings on the screen are a little fuzzy, as well as the icons in taskbar and system tray. Up to today, there are no available Windows 8.1 drivers from ASUS download site for my laptop. Let's hope there will be, someday...
I hope this will help you.