Lack of Father/Son relationship or surprise
A lot of the flaws in this film have already been mentioned: the voice acting, Deathstroke being so weak, Damien being near invincible, etc.
But one thing that really bothered me was this film was supposed to be about the father/son relationship growing between Bruce and Damien along with Damien learning not to kill. Except we didn't get any of that. Talia reveals Bruce has a son and Bruce, with no surprise or real emotion goes "Okay." Treats him like he is another Robin, and after a few "we don't kill" Damien is reformed and doesn't kill. I never got the feeling that anything was properly developed on any level especially emotionally. There was no natural progression. Instead, people accepted things because the plot demanded they accept things.