Time.timeScale = 0; only pauses animations?

To pause all physics and all movement in your game, you have to use Time.deltaTime in your scripts. It would be equal proportional to your framerate and your timescale http://docs.unity3d.com/Documentation//ScriptReference/Time-deltaTime.html

Time.timeScale affects eveything releated with timeScale.

In your situation you can create a coroutine and return 1 yeild before setting timescale to 0.

Something like that. (I have written it with notepad so there might be syntax errors.But the logic should be the same.) Hope this helps. :)

 IEnumarator WaitAndPause()
 {
     yield return null;
     Time.timeScale = 0;
 }
 
 void Start()
 {
     StartCorotuine("WaitAndPause");
 }