But I can't see myself enjoying a pop-up window that would freeze the game every time someone casts a spell or attacks with a cantrip. "Would you like to counter this? ...how about this? What about this then? Shall we counter this one?.."
A mix of conditions and reaction pop-ups might be best. Similar to DAO Combat Tactics, you specify conditions for when a pop-up appears.
For all your spellcasters, simply set the "Lowest level spell to show a counterspell pop-up confirmation window" to 1st or Xth level. There'd also be an option to automatically counterspell if the conditions are met instead of showing a confirmation "yes/no" pop-up.
This also allows you to e.g., set what level of smite is used during opportunity attacks.