The biggest reason the player is able to stomp the AI after an initial difficulty spike in brutal difficulty has to do with the player being more focused on building as much population as possible. It doesn't seem like the AI ever researches cloning or habitat domes until very late in-game. This means they will always trail behind the player in the late game, who is quickly able to build a commanding lead in both planets and population. The AI instead will rush to adamantium armor, which is nice, but pointless when the AI is still using nuclear missiles.
This brings me to my second research suggestion. The AI does not seem to be very good at upgrading old ships, but if you wanted to make the AI harder, all you would have to do is tell it to get fusion missiles ASAP, and antimatter missiles when it can. If the AI had as many antimatter missiles as it usually has nuclear missiles, late-game would still be somewhat challenging. The Orthin should instead prioritize stupendous energy, I suppose, but the AI does seem to do that already, to a certain extent.