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I've always been a fan of playing on manual control and did so in DW once I saw how pathetic the Artificial Ignorance was at controlling fleets, ships and colonies. Sad to report that DW2 is a big step backwards for playing with manual control.

Someone posted that playing on manual control was easy, just set the automation policy to Expert and change two values for ship interception range. That overly simplistic answer was absolutely wrong! All those changes did was change policy positions, didn't do anything to change the far too many things that the Artificial Ignorance controls.

First off I have to change colony automation so that I control tax rate and troop levels. I have to set the resource management to automation but I manually override all of the construction resources and I leave it on automation to control the luxury ones. I have to manually change each one of the construction resource Maintain numbers as the AI uses totally wimpy numbers that are insufficient to the task. Sadly there's no copy to all colonies button the way there is for the race policy screen for each colony.

I let scouts run on auto but have to sometimes set them to manual if I encounter a fleet of abandoned ships as the AI is pathetic at methodically going to each one to wake them up. Now I'm finding artifacts and I find the scouts ignorantly keeping up the scouting as long as it has fuel when the smart play is to get those valuable artifacts to a safe colony where they become functional. I have to watch the artifact screen to see when my scouts have them and make sure they don't drop them off at an outlying new colony instead of smartly taking them to an inner one that's more developed and easier to defend.

I never allow warships to be on auto pilot as they'll be ordered to do really stupid things and will constantly try to retrofit which just hogs up colony and spaceport time doing constant retrofits. Just watching how often my scouts on auto retrofit shows me I'm doing the smart thing. I also keep all construction ships on manual control so I build what I want where I want and don't allow the AI to build things in stupid places where they'll be easy to attack. I can control when I retrofit them so that my retrofits cover many component upgrades instead of every one.

I'm now finding that when I have BB's with the fleet command targeting and countermeasures modules that if I send a ship in a fleet to do an independent job like kill space bugs or Hive and other ships that now those independent duty ships are automatically and ignorantly commanded to go back to the fleet flagship once the task is complete. Sometimes that's convenient but sometimes not and if my ships are on manual control I do not want the Artificial Ignorance ordering my ships around.

Every time I create a fleet I have to reset the fleet tactics so that the fleet doesn't do interceptions at 40% of fuel range, the most ignorant setting of all. I have to reset each fleet to same system so my fleets don't do stupid things like chasing phantoms that are always on the move. When I send fleets into battle I have to micromanage them so that they're not being sent somewhere I don't want them to go. In one case I had a fleet attack some Vordikar around one planet and I set it to the first one in front. When I checked back the targeted Vordikar was dead and the fleet was ignorantly sent to attack some Gravillex around an asteroid field in a lower orbit. I had to then backtrack the fleet to finish off the Vordikar around the original planet target.

If you're a fan of manual control then DW2 is not for you. It's a big step backwards from DW. The Artificial Ignorance has also gotten worse since the original, looks like paradox garbage who puke out the worst AI's in the industry. A pity the devs don't think about making the game easier to play for us manual control players.

I run manual as well, but resource automation and colony funding automation I feel is fine to leave to the AI. I only take control of a few key colonies. The rest I think is pretty OK to leave to the AI. Particularly since it saves on tediousness and there's too few games to justify going full manual on these 2 fields. I'd say leave that part be on auto.

For military aspects I don't like leaving it on auto or semi-auto since I enjoy that too much. Can't help you there really. I think though, you can set your default tactics when you create fleet templates?

For scouts: Good idea to run some scouts on auto and leave some scouts on manual, lingering on the edges of your empire, then send them to collect artifacts, do investigations and so on. You can even do different designs for these, so they have the fastest hyperdrives available while skimping on fuel and defenses.

For constructors: set your empire policy to full manual, then have constructors be automated. That way they'll do nothing else except queue up missions that you order through the resource/special locations screen.

In general, it sounds like you need to experiment with your empire policies a bit. I feel the opposite way: Manual play is a lot less tedious and a lot more fun in DW2 than DWU, and I've played both extensively almost exclusively on manual.