A couple of points that have not been made clear IMO.
Why did Pistorius not call out and say who is there, I have a gun.
This will presumably be brought up when he is on the stand.
If she was in the toilet, was it to get away from him after a row or was there evidence that she had been using the toilet for a pee or poo. If there was no evidence of use was it get away from him and why, picking up on what some witnesses said about raised voices.
Her bladder was empty which defence claim shows she had been to the toilet. From the gunshot wounds though she was standing when hit by the first bullet in the hip. She then sat down on a magazine rack (not on the toilet) and was hit again, once in the head. She also had her phone with her which seems strange if she was just going to the loo in the middle of the night but obviously not conclusive.
There had been an argument heard by neighbours but she had no defensive wounds suggesting there had been no physical altercation before the shooting.
Surely when he got out of the bed he would have noticed if she was there or not.
You would expect so but he claims he was sleeping on the other side of the bed than usual due to an shoulder injury. He was out of bed closing a window when he claims he heard the intruder in the bathroom and so didn't have to pass her side of the bed to get to the bathroom which is why he didn't check she was in bed. How you wouldn't be able to tell that she wasn't in the bed though I have no idea.
Finally it was a secured compound and they were not on a ground floor how on earth could an intruder get in.
Intruders regularly find ways into properties that may not seem the most obvious/easy. He is also said to be incredibly paranoid which could add to his behaviour.