I haven't played in a while so I don't know if some of these are older issues or not.
The AI has serious city building issues. Every enemy city I ran across had like 30+ monuments and almost nothing else.
After the AI researches more expensive equipment they revert to making the smallest unit sizes exclusively. They have very little health and no matter how great their gear they die very quickly from range against cheap archers or in a single AoE spell from a caster.
Casters on auto resolve will only cast magic arrow and do nothing else at all, period. Even if they have an awesome weapon and like 10 action points, or much better spells. The spells (or spell really) cast during auto-resolve also don't appear to cost anything. Mana or SP or whatever it's called doesn't decrease even though the unit is casting magic arrow 20 times per combat.
Auto resolve with a bow equipped on the leader causes strange issues on the map. I don't think the animation is right. The attacking unit usually starts with a bow attack animation, but the defending unit often just runs away on the map (possibly following it's route to where ever it was original going), sometimes like 5 tiles away, then there's a 3 or so second pause before the results show up.
The new higher health amounts are extremely IMBA once units start to level a few times. Once groups of standard units get to like level 5 or 6 their health becomes absurd.