Greetings.
I have updated the plugin to v1.10 and have implemented both of your suggestions. Enemies can now have custom formulas, and I added a new function that you can use to replace a part of a damage formula with the custom weapon formula of the user. Check it out here.
As for swapping out enemy battle animations when they use the default attack, I can't do that as easily, because the damage calculation and the animation happen independently of each other. Specifically, action sequences can call the attack animation before making a damage calculation, so it would show the default animation in that case.
The good news is that YEP_BattleEngineCore already has an enemy note tag to change their default attack animation: <Attack Animation: x>, and since I'm pretty sure you're also using my dual wield plugin, you also already have BattleEngineCore!