My own 2 cents:
I think certain things could use a bit of automation, but for the incredibly vast majority, I'd say not. What I would like, automated wise, is gem-restocking and a way to gather units.
A way to replenish gems quickly for a mass of spell users would come in very handy, at least for me, since I tend to give most of my mages generally the same gems. Not to mention, it would help Mictlan out immensely (I swear, that nation was designed for an OCD player). Maybe even a way to give the same command to more than one commander at a time. Shift+Right click on each commander, give order via key command. All commanders able to use that order do it. Handy for when you have to Call God and then go back to Research or Patrol.
I'd love to be able to set a gathering point or something. Toggle one province and any stray units (those without a commander present) in adjacent provinces migrate there automatically. Useful for gathering up those militia for the next suicide run.
