I have not yet reproduced this on my Ubuntu 21.10 for lack of time, but
I ran into it on a Debian 11 machine I was converting to Netplan and
preparing to port the ifupdown scripts.

I tried ignoring unimportant interfaces, but no dice. So I ran an strace
on /lib/systemd/systemd-networkd-wait-online (attached). I failed to
understand what is really going on, but the program configures a epoll
instance. After some successful use of that something fails to happen
and the two minute timeout strikes. During that timeout, the program is
repeatedly looking at /run/systemd/netif/links/1, but it does not
change.

The machine has four interfaces: lo, ens3, dummy1 and tun0.
/run/systemd/netif/links/2 and /run/systemd/netif/links/3 are ens3 and
dummy1, 4 is probably tun0, being the last created, and the state is
ADDRESS_STATE=routable.

But /run/systemd/netif/links/1 is strange. This should be lo, but lo is 
configured:
1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group 
default qlen 1000
    link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
    inet 127.0.0.1/8 scope host lo
       valid_lft forever preferred_lft forever
    inet6 ::1/128 scope host 
       valid_lft forever preferred_lft forever

but /run/systemd/netif/links/1 is
ADMIN_STATE=unmanaged
OPER_STATE=carrier
CARRIER_STATE=carrier
ADDRESS_STATE=off

So I thought that adding a netplan configuration for lo might help.
Well, it doesn't. The strace is the same, except for the contents of the
netif file.

Please reopen this ticket and push it upstream. There is something
uncouth about systemd-networkd-wait-online's relationship with lo.

** Attachment added: "wait-online.strace"
   
https://bugs.launchpad.net/ubuntu/+source/systemd/+bug/1779340/+attachment/5577039/+files/wait-online.strace

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https://bugs.launchpad.net/bugs/1779340

Title:
  systemd-networkd-wait-online.service Failed to start Wait for Network
  to be Configured with bridge

Status in systemd package in Ubuntu:
  Invalid

Bug description:
  The following simple netplan config results in a 2-minut unneccessary
  delay on boot. Everything works like it should in the end. The bridge
  has no interfaces due to a regression in Ubuntu migrating to netplan
  (see
  https://bugs.launchpad.net/ubuntu/+source/netplan.io/+bug/1779341).

  ubuntu@molnix3:~$ cat /etc/netplan/01-netcfg.yaml
  # This file describes the network interfaces available on your system
  # For more information, see netplan(5).
  network:
    version: 2
    renderer: networkd
    ethernets:
      enp4s0:
        dhcp4: yes
        dhcp6: yes

  ubuntu@molnix3:~$ cat /etc/netplan/br1.yaml
  network:
    version: 2
    bridges:
      br1:
        addresses: [10.1.0.9/16]
        interfaces: []

  ubuntu@molnix3:~$ cat /usr/lib/networkd-dispatcher/routable.d/tap0
  #!/bin/sh
  set -e
   if [ "$IFACE" = tap0 ]; then
    brctl addif br1 tap0
    ip link set tap0 promisc on
    ifmetric tap0 5
  fi

  ubuntu@molnix3:~$ journalctl -u systemd-networkd-wait-online.service -b
  -- Logs begin at Thu 2018-06-28 10:07:29 UTC, end at Fri 2018-06-29 14:09:18 
UTC. --
  Jun 29 13:58:16 molnix3 systemd[1]: Starting Wait for Network to be 
Configured...
  Jun 29 13:58:16 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:16 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:16 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:16 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:16 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:16 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:17 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:17 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:17 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:17 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:18 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:18 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:19 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:20 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:20 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 13:58:21 molnix3 systemd-networkd-wait-online[1468]: ignoring: lo
  Jun 29 14:00:16 molnix3 systemd-networkd-wait-online[1468]: Event loop 
failed: Connection timed out
  Jun 29 14:00:16 molnix3 systemd[1]: systemd-networkd-wait-online.service: 
Main process exited, code=exited, status=1/FAILURE
  Jun 29 14:00:16 molnix3 systemd[1]: systemd-networkd-wait-online.service: 
Failed with result 'exit-code'.
  Jun 29 14:00:16 molnix3 systemd[1]: Failed to start Wait for Network to be 
Configured.

  ubuntu@molnix3:~$ /lib/systemd/systemd-networkd-wait-online
  managing: br1
  managing: enp4s0
  ignoring: lo

  ubuntu@molnix3:~$ networkctl
  IDX LINK             TYPE               OPERATIONAL SETUP
    1 lo               loopback           carrier     unmanaged
    2 enp4s0           ether              routable    configured
    3 br1              ether              routable    configured
    4 tap0             ether              routable    unmanaged

  4 links listed.

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