Problem is, a lot of these perceived flaws are not flaws to other people. Now, you have to be specific as to what you are referring to. For example, the complaint about there not being enough Batman is not a problem to many because it's the character, not the costume that's important to them. Some like the character arc Bruce has, others don't. Some can't understand how Bruce got into Gotham, others don't need it and can easily see ways he got in (ex. what other purpose were the special ops guys getting in to show besides that there are ways to get in while allowing us to have a cool Batman moment where he just appears out of the shadows). On top of this, for a lot of us, we see a few negatives but it is far outweighed by the positives. Of course there are problems, no film is perfect (though, I'd argue that films like 2001, The Shining and possibly Schindler's List and Fight Club come as close as possible) but it comes down to what you liked in it, how much you liked those aspects and how much those flaws bothered you. For example, I wish Talia (as Miranda) had more screen time. She was more of an idea than a character.
But what I liked in the film far outweighs any negatives. I won't type out everything I liked in the film since that'd take forever so I'll just drop my analysis here:
http://forums.arkhamverse.com/viewtopic.php?f=91&t=19163
And I don't bring up in it but I also really enjoyed the score, acting, cinematography, action, effects, production design and pretty much all of the technical side on top of the story and themes.