I think I finally know my thoughts on Batman Vs Superman, and why I think they tried to do too much from the start. I will try to keep this as spoiler free as possible.
I'm going to start by saying I thought Ben Affleck did a fine job as batman. For the sort of character that they were trying to portray, I think he did a great job with what boundaries he was given. My issues with the batman character they chose doesn't really make sense with the batman character. One of the defining points of batman that I feel was always there was his moral code to never cross the line and kill people. There's really no way you can't see that some of the stuff he did wouldn't have directly caused the death of some of the bad guys.
As for superman. I think the superman that they were trying to display was okay. The big issue I had with him is that they repeated what they did in the first superman movie(of this cinematic universe), and had him struggle with his humanity and place in the world. Okay we get it, hes an alien on earth. A bunch of the issues they tried to pass of as major concerns with how humanity viewed him just didn't make sense. They invented an issue where his personal feelings directed his actions, and then tried to turn the result of his actions into this giant political issue, but then did a poor job actually selling that people where legitimately afraid of him.
Lex Luther...oh dear god, why the hell did they have to do that to my poor dear Lex Luther. One of my biggest problems with this movie was their depiction of Lex. I felt he was the saddest excuse of a character in the whole movie. Its like they took the Lex and decided he was the only one who needed a complete make over, and took everything about his character, cherry picked a few parts of him to make it make sense in their story, but then redesigned the rest.
All in all, I feel like the biggest issue that the movie had was that it tried to do much. What I mean by this is the fact that they throw you into the mix, and show you a whole bunch of stuff that unless you actually are an avid batman/superman/justice league fan, you really wouldn't understand what any of it is, and it just ends up leaving you confused. There is a whole bunch of character chemistry that it is showing, that doesn't make sense without any context behind it.
(eg Alfred and Bruce). What I think they were trying to do with this is leave doors open to the follow up movies they have planned, but without that context it makes no sense.
I view it as if you were to watch The Avengers without any of the other movies first. Without knowing some of the backstory, like who Loki is, how he got to where he is. Him as a bad guy with almost no lead-up makes no sense what so ever. He just pops into the universe and is like surprise I'm the bad guy. Or even the Tesseract, you would be left with questions like what is it's purpose, how did it get there, etc. Yes Batman Vs Superman had some of that stuff that related back to the Superman movie, but most of it doesn't make sense without any context.