Suggestion:

   1)  Allow the player to set autoupgrade on / off on the govern / economy screen.  Place the radio button near the "reset all planet to global spending" icon.  When on, everything available to be autoupgraded will be queued to autoupgrade on new turn.  When off, nothing will be added to the queue, but it will not cancel upgrades either.

   2)  Add an "upgrade all" button to the planetary build screen, that queues an upgrade of everything currently built that had an available upgrade.  Player can then rearrange or delete from build queue.

   3)  If autoupgrade on / off radio button on main screen is pressed to go from off to on, you get a pop up.  Option A)  no, sorry, do not upgrade anything.  Option  Pulse upgrades - upgrade everything upgradable in the empire once, but leave the button off.  Option c)  Autoupgrade is now on, will update on new turn.

   Planet by planet autoupgrades can still be turned on / off from the governor screen.

   I can see 3) being useful in several cases, such as switching to and from research projects / birth subsidies / starship building / cash stockpiling to planetary upgrading, or pulsing empire wide upgrades when you get a new tech you really really wanted.

  As it is I hate autoupgrades (mega factories in particular) almost as much as I hate the clickfest of turning it off EVERY TIME YOU COLONIZE A PLANET and then clicking on EVERY BUILDING ON EVERY PLANET THAT NEEDS TO BE UPGRADED EVERY TURN.