Pausing is unintuitive in Unity because you don't control the main loop - all active objects get updated every frame. The recommended way to do it is to set the "time scale" to zero and have menu animations use special timers that ignore time scale. If you control the game loop, you can usually just get away with an "if (paused)" [0].

[0] https://github.com/rameshvarun/marble-mouse/blob/8b25684a815...