This happens because /etc/pam.d/gdm-password is updated and the following line is added:

auth required pam_succeed_if.so user != root quiet_success

The following patch will fix the root login again.

cat gdm-password.patch

--- gdm-password 2014-06-13 23:44:06.000000000 +0200
+++ gdm-password.dpkg-old 2015-08-20 21:56:55.088093540 +0200
@@ -1,6 +1,6 @@
#%PAM-1.0
+# This is kali-root-login's version of /etc/pam.d/gdm-password
auth requisite pam_nologin.so
-auth required pam_succeed_if.so user != root quiet_success
@include common-auth
auth optional pam_gnome_keyring.so
@include common-account

Due to the age of the OS (Kali Moto [v1], Kali Safi [v2], Kali Rolling 2016.x), these legacy versions are no longer supported.
We will be closing this ticket due to inactivity.

Please could you see if you are able to replicate this issue with the latest version of Kali Linux - https://www.kali.org/downloads/)?

If you are still facing the same problem, feel free to re-open the ticket. If you choose to do this, could you provide more information to the issue you are facing,and also give information about your setup?
For more information, please read: https://kali.training/topic/filing-a-good-bug-report/