I get'cha points, Lien. Fair call on all of them. I'll write down my complaints too but I'll do the spoiler mask like you did.
At the beginning when Batman is beating up all the corrupt cops, Alfred tells him off and Batman tries to justify himself by saying they're corrupt and they're in his way. This is showing Batman's inexperience at the time - and his arrogance, because he thinks he can do all of this stuff by himself when near the end of the game, he discovers he can't and he needs help. Despite all the corrupt cops, they still have a duty to do so when they're called upon by Gordon, they do it, but they don't like it. I don't mean to sound contradicting but, I understand your point about this, however I do disagree because of my explained reason.
I found the cameo with Barbara Gordon and her "Maybe we can team up" one day speech really dumb. To me, that was just blatant and poor fan service. It is funny how she immediately trusts the big, dark armoured guy, despite the fact he's broken into the police station and beaten up dozens of cops.
Regarding the corrupt cops... I thought it was dumb about how desperately the game tried to make you dislike these guys and say "Hey, even though they're cops, they're BAD cops" you know? Example - in the police station you enter a room with three cops watching a TV. Listen to them, they're watching a video about homeless people fighting each other ("bum fights") and they're laughing, saying how they hate homeless people. This to me wreaks of desperation of the game trying to tell you that these guys are bad cops and it's apparently okay to cripple them.
And the blood splatter in the police HQ? That was dumb too. Another obvious "Hey, these are bad cops!" flag. I agree, it's funny Gordon trusts these men since they're so obviously bad and corrupt, but I guess it's similar to the movies - he's a good man, trying to do the right thing, wanting to make a difference and is working the best he can with what he's got. Still, I understand and agree with your points.
I certainly agree with your points about Anarky. There was no "choice" there at all, but to be fair... this isn't Mass Effect or anything like that. The storyline is already determined, there's no choice about it, it's A to B, because in this story (like the Arkham games before it) Batman's choice has already been made. I can't imagine Batman letting these bombs go off, with the potential of innocent people to die.
As for Batman's brutal methods of interrogation... yeah, he does that. In The Dark Knight Returns, Batman breaks a guy's leg to get him to talk. Batman also later basically tells the same dude that he's bleeding to death and only he (Batman) can save him - basically Batman's saying "If you don't talk I'll leave you here to die". In the Christopher Nolan movies, Batman regularly beats up guys while interrogating them... he did this to Joker, Bane and he dropped that crime lord off a balcony and broke his ankles. In all honesty - it depends on the writer(s) about Batman's interrogation methods, which makes the character Batman at times inconsistent and even hypocritical. Some people believe because of Batman's brutality, they believe Batman may be sadistic towards criminals. In reality, he tries to use fear - and even pain, to get information. As for dropping that guy off the building into the Christmas tree? Yeah. That was too far. I would have thought Batman would have left him hanging on a cable or something, you know? I don't recall Batman being this violent in Arkham Asylum or City however, again... I raise the point of Batman's inexperience, compared to the previous games. I hope that makes sense?
As much as I love Batman, whenever I read Batman comics or other related comics (e.g. Nightwing, Red Robin etc.) or if I play the Batman games... it's definitely a "leave your brain at the door" scenario.
Batman: Arkham Origins is a good game. However in saying that, just because it's bigger than the previous games does not make it better. I think Arkham City is probably the best Arkham game out. Unfortunately, Origins lacked the same "wow" factor as City did in terms of storyline and gameplay.
Also, the fight with Deathstroke (Slade)? Yeah, pain in the arse... but once you figure him out, he's very easy. I'm not looking forward to fighting him on New Game Plus mode though...