Other than the whole "We are killing you to protect "all life" from being killed by syntetic life" was one thing and completely bad logic loop. its also the lack of what happened afterwards. Also why was Joker running away?? It was like WTF is going on... the ending felt rushed to the point of, "Wow guys did you tack this on as an after-thought?"
Yes the Free DLC helped with that but still makes me wonder, did they really look at and watch it and people agreed that "Yep thats what I wanted" Or did they just find a bunch of yes men. There are reasons, why movies do test runs of there movies with live people. To find out what does and dont not make sense. Just because you konw all the backstory doesn't mean that you present the infomation to the audience correctly. And in this case, if we where talking about movies, It went from an A moive (near block buster status) to B within a few minutes. I think its the same thing that happend with 2001 A Space Odessy. Tho I just pass the last few mins of that to be the oblisk giving him a ton of infomation. Or chaning him into a higher being.
If I where to talk about this like a plane, It would be a plane ride where the inflight movie was good, No smelling gross pasanngers and the inflight food was good. And when coming in for a landing the landing gear breaks and crashs the plane. No one dies but, the only thing you remember about the plane trip is the end when something bad happened.