Help troubleshooting slow startup at boot

Ive been on HA Core for over two years. The other day I decided to upgrade from Ubuntu 18.04 to 20.04. I did a clean install and restored my configuration into a python virtual environment. Everything works fine but I have noticed one issue. It seems that after a reboot of the system, the first time HA starts it takes upwards to 3 minutes. I have turned on debugs but I have not been able to find anything meaningful to point me in the direction of what is causing this hang. I thought this was due to HA starting too early in the systemd process, but I moved it to the end and I still see the issue. I even disabled HA in systemd, a manual start of HA after the system has booted still suffers the 3 minute lag. Now for the kicker, subsequent restarts of HA are very quick, 10-15 seconds! Its only after a system reboot do I see this hang. When it occurs these are the messages I see:

Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 INFO (MainThread) [homeassistant.setup] Setting up mobile_app
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 INFO (MainThread) [homeassistant.components.remote] Setting up remote.apple_tv
Nov 13 07:28:05 hass hass[657]: message repeated 2 times: [ 2020-11-13 07:28:05 INFO (MainThread) [homeassistant.components.remote] Setting up remote.apple_tv]
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.light] Setup of light platform mqtt is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.binary_sensor] Setup of binary_sensor platform mqtt is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.sensor] Setup of sensor platform darksky is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.sensor] Setup of sensor platform tautulli is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.sensor] Setup of sensor platform mqtt is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.sensor] Setup of sensor platform command_line is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.sensor] Setup of sensor platform snmp is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.sensor] Setup of sensor platform iqvia is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.media_player] Setup of media_player platform apple_tv is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: message repeated 2 times: [ 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.media_player] Setup of media_player platform apple_tv is taking over 10 seconds.]
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.components.media_player] Setup of media_player platform vizio is taking over 10 seconds.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 INFO (SyncWorker_18) [ciscomobilityexpress.ciscome] _call_api : https://10.7.7.4/data/client-table.html?take=1000
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 INFO (SyncWorker_11) [homeassistant.loader] Loaded sonos from homeassistant.components.sonos
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 WARNING (MainThread) [homeassistant.bootstrap] Waiting on integrations to complete setup: hacs, device_tracker, mobile_app, nws
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 ERROR (MainThread) [homeassistant.components.media_player] Setup of platform vizio is taking longer than 60 seconds. Startup will proceed without waiting any longer.
Nov 13 07:28:05 hass hass[657]: 2020-11-13 07:28:05 INFO (MainThread) [homeassistant.setup] Setup of domain mobile_app took 0.1 seconds

At this moment when these messages appear, the HA fronted becomes available. As a troubleshooting step I disabled 90% of my configuration.yaml file, but the problem still persists.

How can I best troubleshoot this issue?

There are several integrations like MQTT that are not configurable via the yaml file, is there a way I can disable the MQTT integration? I suppose you have to delete the integration? just had an ah-ha! moment Perhaps I will take a backup, and disable the integrations and perform a few reboots to test. Sorry for the rambling, it helps to type these things out, more to come…

Are you saying that the first time you boot up home assistant with a new system, it takes awhile to start up? If so, this is expected especially if you have a lot of integrations configured (either through UI or yaml). The first time it starts up, it has to download and install all python libraries for home assistant and all your integrations. This can take a long time depending on your internet connection, cpu speed, etc…

Sadly, No, its every system reboot. I have isolated the issue to something in my configuration.yaml. I did about 10 reboots this weekend, and I came close to finding it. I will just need to continue to isolate sections of my config, rebooting twice to double verify which integration is causing the issue.

ever find what was causing the slow reboot?

No, but I have since moved to HassOS running on KVM and the slow startups are gone.