I am recently working on a "realtime with pause" style grand strategy game using my own engine (think Europa Universalis, Crusader King, Hearts of Iron).

The trick is to separate the logic simulation from other game loops (rendering, UI, input, sound, etc). So when a player pauses the game, everything else still more or less works. And the logic simulation should be able to take user "command" while being paused.

Most commands should mutate the game state and reflect in the UI immediately. A few commands that have to wait until the next tick should at least acknowledge the action result.