I'm pretty sure in the years of surfing I've done I've read one or two pages on Moo3 getting some fan-made mods/patches that fixed a lot of its problems.

Google searching is leading me to the first two games, so I'm left to asking around.

Probably http://www.gog.com/en/forum/master_of_orion/master_of_orion_3_tropical_mod_install_instructions/page1 is what you're looking for.