Fallen Enchantress by Stardock did something that I've not really seen in other 4x's, unique zones on the map that have a theme and story. AoW4 kinda has that with Ancient wonders but I'd like to see this expanded upon in AoW4, leaving the Ancient wonders as they are and making a collection of provinces on the map into a unique area. Expand upon the theming of the hostile spawners and give each spawner type a mega city. These are neutral to players so won't hinder army movement on the map. They have quests in alignment with their theme (Undead one could be first player to kill X units) that when complete give bonuses and at top level block other players from gaining more bonuses and they become allied. Could have special skills unlocked with Imperium ala allied Umbral cities. Gains towards unlocks apply regardless of if you've discovered the city but you don't get rewards until discovered the city (so as to not allow an early scouter an unassailable lead). This also functions a bit like the quests in Endless Space 2's tech tree. Astral themed unit city could be "cast X spells either in strategic or tactical". Animal could be "donate X food" (inhibits own city growth).
#Map additions akin to what Fallen Enchantress did
stray comet
And of course you could just conquer them, but they'd be scaled to be a late game challenge