Same problem here - upgraded to Windows 8.1 same day I got my laptop with Windows 8 and loading times are very disappointing.
Each load and shutdown were taking about 3-5 minutes, rotating circles are going fast as they should, but before them (in case of boot) and after (in case of shutdown) there was 3-5 minutes of black screen with laptop fan and power indicator being on.
I've managed to fix boot time and reduce black screen to 10 seconds by removing Intel HD graphics and Nvidia drivers pre-installed by Acer and installing fresh ones from Intel and Nvidia websites, but this did not affect shutdown time, it is still taking 3-5
minutes of black screen to shut down.
Now I just hold power button and force shutdown as soon as screen goes black, this does not affect anything and Windows does not see this as a crash.
Still, would be nice to fix this.