The story you told is actually non-sense. Unless you throw away balls, there is nearly no chance that Mewtwo will run.
I caught 3 out of 3 Mewtwos already and hoping to catch my forth tomorrow.
Tips is that be calm, take your time. You will probably be nervous in throwing the balls. There has been some changes in Mewtwo distance, so I'm not really sure which pokemon is comparable.
Another fast tip is that don't throw the ball too early, since there will be some time interval before the circle appear after Mewtwo moves his hand. You will kind of get the timing soon as you will face him in the catch screen. So, again be patient!