Research and Ship Building come to mind for two things that require way too much clickage
You know what also requires lots of "clickage"? Sending units to attack, building your defenses on a new planet, moving your forces around to planets that need defending, etc, etc.
Yea, I'm sort of making fun of you, but more-so I am pointing out that removing almost all "clickage" will move the game away from an RTS and into a programming game. Don't get me wrong, programming games are fun too, but AI War was never supposed to be one (despite its name
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There needs to be a line where automation needs to stop or risk shifting the genre or paradigm of the game. Of course, it can be hard to find where to "draw the line".
That said, I wouldn't mind a separate "research" screen or panel or whatever that is available as long as you have at least one science lab in supply on at least one planet. That way, you don't have to try to find a research lab somewhere in your empire just to research something, where it doesn't really matter what science lab is chosen.
On the other hand, it does matter which shipyard (or whatever) builds a unit, so having a separate "build panel" would not work so well. One nifty way to help ease its use that has been proposed it "ship builder queue templates". Its somewhere on mantis, so vote it up if you like the idea.