So, I decided to give this a try again since GOG granted me a discount on the gold edition and it's endorsed by some prestigious Codexers. I just did the Conquest mode and the first thing that immediately stands out that could've been handled better is the two factions. As a "genius strategist", Kyros should know that 2 groups can not regulate themselves, you absolutely need a third one so that if one of them becomes too strong (for example, say, an especially gifted agent prefers one of them, like, you know, us) the other 2 can join up in order to even the scales. If the writers wanted to explore the ramifications of imperialism and authoritarianism, they shouldn't have focused on you trying to subjugate the last pitiful remnants of a minor rebellion that have absolutely no chance against the overpowered magics of Kyros, but instead focus on inner squabbles after the regime has won. Outside of that, always having to choose between the chorus and the disfavored (with one exception) felt forced, which is exacerbated by you not having any information before deciding on your next move on the map (like between the library-citadel, Azur, and the fortress). Speaking of the library, the decision to burn it to the ground came completely out of the left field, we were there to steal knowledge, not commit arson. We didn't need to be there at all for the edict to do that. My last observation is Kyros feeling overpowered and that rubs me the wrong way.
The other possibility would be that Kyros is not actually a good strategist but relies entirely on overwhelming force and those edicts, which allows one of the armies to become too powerful and turn against her/him. That would've been a more standard story, but there's nothing wrong with standard stories told well.