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It seems the strategy game market is all into complex tech trees and insane amounts of learning. Master of Orion 3 has an AI for practically everything, which makes the game sort of unique.
While games such as Hearts of Iron 3 have automation in them, they don't really invite you to go ahead and allow the AI to control those parts of the game because ceding control of anything in that game cedes control of the gameplay experience.
Master of Orion 3 is much different. You control what you want to control (and you can micromanage basically everything), and you get as reward what effort you put into the game. For instance, I personally don't like tech trees, so I let the AI do that for me. I do all the scouting, do about 30% of the resource management, and do all of the combat. This provides me with a unique experience for myself that others might find less enjoyable. For others, they can let the AI control OTHER things, and have fun that way. For this reason, I call this a flexible strategy game.
One reviewer mentioned that you can just hit "Turn" constantly and still win. This is pretty much true, but this is a game about learning your own boundaries and expanding your strategy skills through taking control. Likening the mindless atitude toward the game to platforming games, would you like Super Mario Brothers if there was a pipe at the beginning of the first world that led you to the end of the game? Chances are, you'd try to play the game by going through the levels and not put up a stupid review saying it was too easy for you because you knew how to jump and press down.
For all those complaining about the game being buggy on release, this is the latest version (1.2.5), so those comments are only relevant to year 2003.
As for modding the game, there are a lot of bugs that were fixed by the community as well, which means that you probably should go through a little effort to play this game to it's highest potential, but isn't that the same as say Freespace 2, which is highly acclaimed as one of the best games ever?
If you want to play it right from GOG.com, here's a little list:
1) Install GOG's package; this installs MOO3 1.2.5
2) Download the Tropical Mod from http://www.moo3.at/mods/
3) Extract the contents of the Tropical Mod into a NEW DIRECTORY.
4) Delete "MOO3.exe", as this is a modified version of the original, CD checking EXE. They installed a bunch of patches, but those patches and patch software are included in the package.
5) Copy the contents over to your MOO3 directory.
6) Run "Moo3Patcher.exe"
7) Hit "Install" on the DLL installer.
8) Step through all the patches one by one, hitting "Patch" to patch GOG's EXE.
9) Run MOO3.exe
This worked fine for me even in Linux using Wine 1.1.42.