At the moment i really don't see the point for the massive distinction between the two. All the differences seem at best cosmetic and at worst just arbitrary. I don't see what the fact that only empires can build a +2 mana building says about their philosophy, or how different numbers for the housing buildings make them a fundamentally different gameplay experience.
I get that it's good to have ideological opposition between factions, because it nudges them towards war, which (turtler as i am), i feel bored if i can avoid for the entire game. I also get why neutral was removed, because in GC2 it was kinda overpowered.
But to my mind, everything the game seems to be doing at the moment would be much better served by merging the tech trees into one and adding branching options (ie, choose between technologies that drain power from the land, or that rejuvenate it). If you want to leave a mechanic to create an "us vs them" mentality, then separate that into cultures and give the empires "Eastern" cultures and the kingdoms "Western" cultures.
Racial differentiation is better handled by stats. Multiple tech trees are a kop out to me because the nature of science in your world shouldn't changed based on who you're playing. More than anything, a single tech tree would be easier to balance and allow players to talk to each other far better. And I can play the same faction in different ways.