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Interestingly, this problems seems to have many fixes/causes. While none of the above helped for me (encountering the same problem), I fixed it by switching from the X.org graphics driver to the propietary nvidia driver that is recommended under software&updates. Since then, reboot works flawlessly.

My setup: Asus G Series Laptop G501VW, with Nvidia 960M graphics card.

Same problem here on my laptop. After some observation, I found out that it has something to do with power saving mode specially automatic suspend.

Go to Settings > Power then turn off all Automatic Suspend options. Also choose Blank screen to Never.

Till Ubuntu team will figure out why suspend mode is interfering with shutdown process, this solved my problem.

Hope this helps

Had the same problem on a brand new ASUS N705u.
Found had to do with how the video driver installs which causes a conflict with the "secure boot" function of the BIOS.
Solution: Turn the "secure boot" function off until other solution will become available.

I had this problem and in my case it seems to be related to the Intel Bay trail CPU which is causing some firmware bugs.

Anyway I have a solution which isn't the best but good enough for now

Solution:

• 
  

  Open the terminal and run

  
  
  

  sudo -H gedit /etc/default/grub
  
  

  
  


• 
  

  Edit GRUB_CMDLINE_LINUX_DEFAULT="quite splash" so that it says

  
  
  

  GRUB_CMDLINE_LINUX_DEFAULT="intel_idle.max_cstate=1"
  
  

  
  


• 
  

  Save and exit, and write the changes to GRUB's actual config file:

  
  
  

  sudo update-grub
  
  

  
  


• Restart your computer forcefully one last time

Let me know if it worked or when you have a better solution

Try a couple of sudo reboots from terminal to see if it clears things up:
1st to try, reboot without writing wtmp file:

sudo reboot -d

If that reboots successfully then try your natural close down. If it doesn't reboot, try forced reboot:

sudo reboot -f

If this was an upgrade from 16.04 to 18.04, it may be worth considering a clean install.

There are scores of scripts that run when you shutdown. I'm still on 16.04 and for me these are the ones in /etc/rc0.d (which are really links to /etc/init.d). One of them may have a long delay set in what it does for stop.

AFAIK these scripts are run in alphabetical order, so you can insert a few that would just log their execution somewhere, helping you spot where the delay is.

After doing more testing on two computers found it is in fact the Wifi Manager and the way it connects / identifies with the network. On two identical computers the problem disappears once the Wifi manager is turned off. Also tried USB Wifi dongle which worked on one computer but once again caused system to freeze at moment of registration on network. Have already tried a different Wifi manager with improved conditions.
Also noticed in BIOS if secure boot is disabled then there is a list of drivers rejected bi BIOS due to security issues. Perhaps this is the underlying issue related to the Wifi manager.

I had success turning off usb 3.0 driver in bios, not ideal, but it is fixed until more research is done.

My system is an older Dell Dimension E521 desktop, dual core, with Lubuntu 18.04, 64-bit.

In /etc/default/grub, I removed acpi=off and the system started behaving normally.

More specifically, I changed this:

GRUB_CMDLINE_LINUX_DEFAULT="quiet splash noapic acpi=off"

to:

GRUB_CMDLINE_LINUX_DEFAULT="quiet splash noapci"

Now my box once again shuts down when I tell it to, and is refreshingly responsive.

I noticed that it happens to me too if i use my laptop for more than 10 hours, the gnome-shell uses more memory with time starting from 200 and going up to 500, firefox too starts with memory usage of 150 and goes all the way up to 900, restarting my laptop every 4 to 5 hours solved the issue of shutdown freezing for me I hope it helps you.

I had the same problem after installing 18.04 on a Fujitsu Scaleo.

During the install I had to add the acpi=off to be able to install Ubuntu because of a conflict with the Intel 82G33/G31 Express Integrated Graphics Controller.
After that Ubuntu would just halt at System Halted when I shut it down.

In the end I changed the BIOS ACPI Suspend Type from S3 to Auto. I did this in Power Management.
After this the PC would power down and I could even remove the acpi=off from Grub.

I had similar problem with ubuntu 18.04. I installed nvidia driver and now it works fine. Install your driver as described in https://linuxconfig.org/how-to-install-the-nvidia-drivers-on-ubuntu-18-04-bionic-beaver-linux

I don't know why but for me, when I remove whole "quite splash acpi=off" and leave it blank, the issue is gone. Now my PC boot and reboot smoothly