How do I connect to L2TP over IPsec using Network Manager?
This appears to be because you just installed the command-line side of NetworkManager's L2TP support.
In order to use the GUI to configure L2TP VPNs as well, you will need to install the network-manager-l2tp-gnome package like so:
sudo apt install network-manager-l2tp-gnome
Following this, a restart of nm-applet may be necessary to make NetworkManager see the change. In order to do this, just run the following:
killall nm-applet
nm-applet &
disown