I would really prefer and appreciate a popup of some kind to allow me to pick reactions to use.

However, if that is out of the question would a script system for reactions be out of order? I'm thinking something like Dragon Age 1 (with advanced tactics mod) - where you can set a few "if X then do Y". That could work well for reactions.
If enemy hits me within X armor class THEN cast shield.
Use Smite if I score a critical hit and enemy is > X% health.
If enemy moves out of my threatened area, then [Attack] or [Cast spell] if spell slot is available -> chose spell AND enemy is >X% health.

Could become too convoluted, but it's the only way I see allowing for complex decisions without allowing the player to make the decisions (which, again, would be much preferred).