Enemies and anomalies were randomly placed, explaining why we had any number of buried anomalies and enemies spawning inside the geometry for the buildings.
The dialogues were done via template and had random talking heads assigned to them, explaining why we were getting hails from borg claiming planets as spoils of war... not to mention hails from targs.
No one did any of that by hand. It did however have to be fixed by hand.
The system just flat out never worked very well, which I guess is why it was entirely abandoned and we never saw any more additions to the Exploration Clusters. Would have been nice had they fixed the tools instead of tossing them on the Pile of Unrealized Ideas™.
We've been told that those were retouched by hand. The problem there was that they probably gave somebody about 30 days to inspect 8000+ missions, since they were not procedurally generated on the fly but were pre-created random missions that had to be hooked up. And whoever was reviewing enemy placement probably got a sense of false confidence, checked one group outof five and said, "Looks good to me."
I have some ideas for randomized content. But one of the first rules should be, all randomized content should use the same physical terrain and spawn points. You can change the ground and sky textures, the weather, etc.
But if you're going to randomize a bunch of content, the way you do it, in terms of protocol, is to make a GOOD map and place every possible spawn on it at once. That's buildings, friendlies, enemies, trees, etc. Then you randomize what DOESN'T spawn on the map and on top of that you have each map contain MORE THINGS to do than the player is required to do so that there can be optional elements. You also randomize thingslike weather, lighting, ground textures, color schemes, etc.
Randomizing terrain, however, looks sloppy without heavier retouching and is akin to developing technology to randomize a theatrical set. It can make for a lush/interesting environment but it lacks flow and it lacks narrative.