To reduce micromanagement I tend to leave colonization (after the first few), transports, and minelaying (if I bother) to the Ministers. I find planet creation and nebula destruction likewise tedious enough to automate occasionally; and I'd add black hole destruction to the list, if I weren't concerned that the SM ships probably would go through a damaging warp point when on autopilot.
Is that optimal? No. But I'm the sort of chap who hates to have to pull out a calculator (or spreadsheet) for a game to find optimal values... calculating troop morale in _Empires in Arms_ is annoying enough.
Then, I also tend to have a fairly busy research queue -- often a full one during the early/mid-game, when I'm going full-bore for infrastructure, so I don't have to check that one often. Intelligence, once in place, usually is given a repeating queue involving intel sabotage, crew insurrection, and counterintel, so that's low maintenance as well.
I'm with suicide_junkie when it comes to filling up build queues on new colonies. I'll pack 'em with facilities first; they don't have the pop to spawn off new colony ships (well, unless I'm Organic and there's a replicant center in the system, and I'm feeling particularly Hive-like), and I really normally don't have that much other ship production near frontiers; rather, more towards interior systems closer to mustering points where I can assemble/train fleets (when, say, you're going up against Temporal ships, which possibly have Event Predictor III's in their home systems [+30% combat bonus], take every bonus you can get...).
So I don't end up clicking *that* much... and if Aaron ever adds a 'Skip Minister-Controlled Ships', I'll be clicking even less.
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-- The thing that goes bump in the night