I mean seriously. For my Sorcerer in Solasta with Counterspell and Shield, the number of times the popup occurs is minimal, and when it does, you WANT it to pop up.
Enemy mage is casting Lightning Bolt, about to fry your entire party because you mistakingly put them all in a line. Popup. Counterspell? YES!!!!! THANK GOD!!! Animation of my Sorcerer casting Counterspell. Lightning Bolt dispelled.
I will ABSOLUTELY be okay with the game pausing for a brief moment to give me a popup to let me counter that spell.
But, yeah... minor spells and abilities... no. Let's do some sort of Scripted Reactions or something to avoid popup windows for those.