Network Manager not working anymore (Ubuntu Core 16)

It is possible that there is a conflict between the wifi configuration from console setup, which uses networkd, and the one from NM. I recommend that you remove the wifi connection from networkd before configuring one from NM - you need to use one or another.

Also, please do not install the wpa-supplicant snap - you do not need it. NM can use the one included in the core snap. The wpa-supplicant snap is of interest only if you want to use WoWLAN.