I re-installed MOO3 after about five years of not playing it, and was immediately reminded of its many broken features and awful problems, plus the enormous degree to which I had modded it to get around those.
Don't try to play it straight from the install CD. Go here instead:
http://www.moo3.at/mods/
and install either the Vanilla or Strawberry mods. I recommend the Tropical mod but you need at least Vanilla or Strawberry just to make the game work.
If you want to remove a tech from the game, insert the following into column H of the TechTables.txt file at the appropriate line for the tech:
Antar_99
instead of making it only a level 99 tech. Making it an Antaran tech too means it can't be discovered from a newly discovered planet.
The reason for this is that random advanced techs are often discovered when an empire destroys the Guardian for a particular nuked-to-glass former homeworld of an old race's empire. The AI's will then trade that tech around among themselves (after stealing it from you if necessary) so it might get into the game even if no race can research it. I vaguely recall a spreadsheet entry which restricts a given tech from being randomly discovered, but also vaguely recall that this affects only the generic random event which sometimes happens on a first discovery of a new star system. There is another special event which happens upon defeating a Guardian, and it provides more advanced techs. I find it safer to make all undesired techs into Antar_99 so no random event, period, can introduce them.
You will find micro-management of new colonies an awful chore in the middle and end games. I recommend, after installing one of the flavored patches above, that you make the following buildings into Achievements instead so they don't have to be built on colonies:
Lines 554, 555 and 556, which are Astro University, System University and Imperial University respectively. Change line G to:
Achieve
It is also an incredible, and slow, pain in the rear to build the various sorts of spaceyards on each new colony. I recommend you mod them so empires need only build the very first yard.
Change line 439, column K's entry for:
Hull_Bld+=1,
to:
Hull_Bld+=10
And add:
Antar_99
to the Column H entries for lines 440-448.
Note that the Strawberry mod allows 14 hull sizes, not 10, so, if you use the Strawberry mod, you'll have to change line 439, column K, from Hull_Bld+=1 to Hull_Bld+=14, plus hunt down the four new space yards to add Antar_99 to all their column H's.
Just because an empire can build any size ship hull at the beginning of the game doesn't mean they have discovered the tech for that hull size. There may be some downside to having only the hull size tech determine that, but the horrid micromanagement for building all ten different space yards on new colonies/newly conquered planets in the end game is such that I use only the basic spaceyard for the whole game.