I don't think timed prompts would mesh well with the game flow. You'd have to pause the game for 2 seconds to wait for user input whenever reaction is possible. It also adds a real-time element to turn based game. It would require very good automatic camera control and clear signaling what the enemy is doing, if user is expected to react in 2 seconds and decide what to do. Its bound to lead to "feel bad" moments where you miss the window.
I think automatic reactions on rules you've decided in advance keep the game flowing best. Perhaps there are some rare reactions which give you a prompt, because they expend valuable resources. For example you might not want to spend Counter Spell on rangers tiny buff when high level enemy wizard is next. So, a hybrid approach where most reactions are automatic such as AoO, Shield, Feather Fall to keep the gameplay smooth, but prompt for "more expensive" reactions?
