I saw pretty much the same shocking under-utilisation of tiles.  The only difference between Intelligent and Ultimate is that leg-up in terms of abilities.

I'm going to cross my fingers and hope that limiting farms to one per planet will help the AI avoid stupid mistakes like these.

Lone transports are a pet peeve of mine.  When I go and invade, I usually (except that time when I was getting stonewalled by Yor defending troops) take enough transports to finish the job.  The AI sends its transports unescorted at a target without even considering how likely it is to get shot to pieces before it even gets there.  It only has some success with this strategy when there's a swarm wiping out defenders.

Also in the poor war-fighting category: the tendency of some civilizations to send fleets from halfway across the galaxy to destroy an undeveloped starbase.

The obsession with starbases needs to be worked out.  Whether it's sending fleets across the galaxy to pick off a worthless base or sacrificing half the armada against a well fortified base, the decision process needs improvement.

I have some others.

1 - The decision process for choosing targets needs help in general. Right now it's basically "is my fleet stronger?"  If yes, attack.  If no, find another target.  Sounds good, perhaps, until an AI sends its entire armada across the galaxy while a couple powerful enemy fleets pillage its core systems.  I mean, they fly their fleets right past the incoming enemy because they are individually too weak to stop them.  Two or three fleets in succession, though, could stop the threat.  Likewise, the powerful fleets ignore the outbound enemy because they are targeting the lone defenders.  Really? Our fleets just sail right by each other because we figure we'll have better luck against each others lightly defended worlds?  Oh boy.

2 - Speaking of lightly defended worlds . . . nuff said.  In my Kushana Initiative AAR, however, my conquest of the Yor systems was slowed significantly by large fleets of defenders.  Like 3 to 6 per planet.  Made for slow going after I captured their Orbital Command Center.  Highly unusual in my experience.  They didn't have much to do with their ships, so I guess they just let them pile up.  They could have done a lot of damage if target priority were better, as mentioned in 1.  Actually, they probably could have turned me back if they made a focused effort to stop my fleets and transports instead of . . . wait for it . . . sending their remaining fleets on a 10 week journey to my not-so-lightly defended worlds.  Sigh.

3 - The thing I was planning to post about in the first place.  I've seen numerous cases where an AI that has been slow to militarize is attacked by the local bully.  In my mod, the weaker AI is usually very quick to get rolling with weapons, but also usually makes the stupidest choice possible.  So the bad guy comes in with, say, guns and armor.  Does the newbie take advantage of that and go for missiles or beams?  Of course not.  Guns is the flavor of the game, so they start building fighters with 1 gun attack to counter the invaders coming in with . . . 2 armor?  That's not fighting uphill, it's grabbing a sled and hitting the slopes.  The much vaunted ability of the AI to adapt to what the enemy throws at it is sorely lacking.

Ok, enough for now.  I don't mean to simply beat up on the game, but these are some pretty spectacular failures that would need to be addressed for a GC3 to be an excellent game.

The willingness of the AI to trade away half their recently colonized galaxy for some techs and warships during a period where no warships are necessary (for instance, when there is no war). The AI needs a bit more intellect when it comes to valueing future gains.

The Troop Transport thing makes fighting an AI that is vastly, vastly more powerful than you not a lost cause, the AI is quite bad at exploiting crushing military advantages for actual territorial gain. As for AI troop transport preferences: I find that they have the tendency to try to retake planets they lost first, before invading other planets. Even when they lost the planet they try to retake a long, long time ago.

Edit: I'd like to stress, by the way, that inspite of its flaws, the AI in Galactic Civilizations II does a much better job than any other AI I can recall in any strategy game (or any game short of Chess) period!

Pretty sure I've never seen it, either, but I have seen the AI build over the Recruiting Center and occasionally economic structures.

All I can tell you is that I didn't change a thing in the improvements file.  It doesn't make any sense.