I think the AI in general needs a major overhaul. In this day and age the AI should adapt to your playstyle to keep it challenging. It makes too many dumb mistakes and it’s very formulaic and predictable in what it does. It doesn’t collect favour intelligently, it doesn’t use all the unique strengths of its Major god, cast God Powers poorly, doesn’t research basic upgrades etc. Don’t get my started on building and wall placement..
Surely they could get AI to make AI. An adaptive one that learns from you as you play.
Those are neural networks 
For AI to learn it needs additional and permanent memory (big servers). The moment you exit the game everything gets reset and it stays a default AI algorithm. For me AI player is okay (of course it can and should be better), but I/we demand that some bugs and issues like this get fixed. The AI player in the old Age of Mythology has the exact same problem. Villagers run away as soon as you touch them without the AI checking the situation.
I think 1 is a bug in the way villager behavior is coded, probably also some pathfinding issues mixed in. Even you own (human player) workers will behave strangely, if you pay close attention to them you will notice all sorts of weird stuff, like picking “interesting” paths to the drop off point, wondering out on the map and ending up in weird places, asking them to gather one resource but will instead gather something else nearby and so on. My guess is that the villager auto management isn’t fully turned off when you actually turn it off.
The herd spawns at this distance on any map, which I personally don’t like. But the fact that wolves and monkeys spawn in the water is bad.