I hate when you type something extensive, and then when you press post it deletes it all because your token has expired... I'll try to re-type it without the qoute's since it took a long time to set up.
Andrea doesn't have all the information needed to make accurate decisions on what each character is doing. If you take into consideration the blind spots she has with regards to the governor it makes sense why she might still trust him. The heads in the jar doesn't necessarily make him a nut job - his description was reasonable, he used them to numb himself to the horrors of the outside world. Keeping his daughter is just him not being able to put down the greatest love of his life. Fighting michonne makes sense because Andrea has never gotten a full explanation of anything from her, so her actions seem cryptic and at times contradictory or chaotic. Her main fault is that she wants to trust people, and she makes decisions about things without having much leeway for new possibilities. As seen by her response to the girl at the far attempting suicide - "well now everythings hunkey dorey, she'll never do it again! she wants to live!". It makes sense to her because that's what she's experienced and her experience and understanding is what feels correct to her. Also when the doctor/scientist tries to see if there is latent memories in the patient when he first turns, her response is "I'm sorry, scientific method of experimentation? They have no soul. I know because I've seen one once. Scientific method is stupid." It doesn't make her stupid it just means she's stubborn with her opinions once she comes to them, and many of them are reasonable given her experiences.
Maggie's shooting does become sloppy when it's aimed at people but there are good reasons for that. There are two things that are asked/happen when shooting at people that no longer happen to them when shooting at walkers:
1 - "am I making the right choice?" killing a walker is always the right choice. Killing a living person? answers vary.
2 - People shoot back. Walkers do not. You don't have to fear a walker that's 100 feet away if you have enough ammo, you have to be very afraid of a guy with an assault rifle.
I don't think Merle has toned down as much as had to accommodate and deal with being part of a hierarchy. Before he was an outlaw and money still existed. He could rob a liqueur store or sell drugs and make enough money to be completely self sufficient, and anyone who met him needed to be afraid of him, not the other way around. That world doesn't exist any more and it means he has to rely on other people to a degree. If he runs his mouth off and gets kicked out of woodbury he'd be alone in zombie territory where no one cares how big of a badass he is and he has no where to turn for food/shelter. That calls for some filtering. But that doesn't mean he's changed, he's still racist (as seen when interrogating glenn), he's still ultra violent (as seen with glenn, the italian guy, etc etc), and he's still not great towards women. He's still kinda dumb, as seen by him telling the governor Michonne was dead without any evidence, and just hopeing he'd beleive it. Everything he was is still there, his actions just have direct ramifications that he can't ignore anymore.
There are two things that have remained consistent with Merles character as far as his underlying loyalties and MO. He only becomes conciliatory when his life is under threat and he has no options, and he wants to be at his brothers side. In Daryls hallucination when he fell on his own arrow Merle was both degrading and supportive. Even though he made fun of daryl it seems like Merle has pushed Daryl to be a survivor and to be self sufficient throughout his life. In that way I don't know that Merle would ever go against him. Not when it counts.
The thing about the Governor, where Merle is concerned, is that the Governor has some pretty strict rules about who he lets in and who he keeps.
-He doesn't like people who have a group hierarchy that he didn't create - as seen by the destruction of the military group. He wouldn't have been able to break that chain of command that was formed pre-woodbury, they could have taken the town if left outside and could have taken it from the inside out if brought into the fold.
-He doesn't like expertise that's outside his direct control. The group took the prison and that makes them ultimately dangerous since they could take woodbury as well, and the military group had the same problems.
-He doesn't like connections that extend outside his walls. That the military guy had a group on the outside was a threat. They would have come for him, and that would have threatened his control of woodbury. The link between maggy/glenn and the group was the same thing. The link between merle and daryl immediately put's merle into a dangerous category - he might leave to go find him and link an outside group to woodbury, daryl might come to woodbury with an outside group if he know merle was there, merles loyalty might split as he tries to defend his brother, etc. If daryl had never popped up merle would have probably remained at the governors side until he messed it up in another way.
Tyrese's group mirrors Ricks in a lot of ways. His wife approaches communication with outside elements harshly. The father son have reactions similar to shane (overly violent). Tyrese tries to communicate in a level headed pacifying manner with outsiders to secure food, shelter and stability for his group. Tyrese is an ideal addition to any group - he contains negative elements and helps to nullify conflict, he makes bonds readily while also being a strong fighter and leader. The rest of his group really needs to get their communication style and expectations in line with him though, or else their going to end up like Shane did. You try to start fights long enough and eventually ones going to come to you.
Axel.... is a terrifying internal element of this story. I've read enough about the comics to know that he'll probably end up taking the place of a really unpleasant story line on the comics. Everyone has a different criminal past and asking what each prisoners were might not have gotten them a straight answer. Oscar (the one who was shot during the invasion of woodbury) was breaking and entering, a burglar. We don't know what axel's was. He might have been a serial rapist or pedophile. Either way his interaction with the women in the last scenes of the episode put him in a category in my head that needs to have a gun trained on him at all times, at a healthy distance. He presented attitudes and perspectives that are dangerous in their disregard for personal space, social structure, and social moires. Despite a common phrasing that it's the end of the world and morality doesn't have a place - it does. It always does. "Only god can judge me" is the credo of sociopaths.