dreman9999 wrote...
There generally 4 themes in ME as a series.
The morality of freedom vs control
The morality of advancement.
The morality of ends vs means.
the issue of organic vs synthetic.
You are taking them out of context. The organic vs synthetic theme is always a solved issue within ME and so it is not a main theme-it's like an overblown side mission. The ends vs the means is only paragon vs. renegade and every story has that as an element-it adds to the conflict. It's always this in almost every story because it's about solving a problem, meeting a goal and how the protagonist does this. It's not a main theme, it is a story element.
The validity of advancement is a theme, but it's abandoned as a concern at the end-to make a choice you basically have to not care about it because you are denying it's relevance. Every rational person along the way stated that advancement had problems-and it wasn't its morality. It was its effects. It isn't that it's immoral to advance people, it's that it harms them in unforseeable ways. It's not immoral to give a family with a kid marbles to play with. It's harmful to do it if the kid is not of an age to be playing with marbles or if the kid just likes to throw things. If you don't know this will happen you should not give the family marbles for their kid.
This is the thing about advancement. You don't know what effects it will have. You may be doing it to even help people, so you aren't being immoral. You are being stupid. That's what happened to the Krogan. They were advanced to solve a problem. But, the advancement they were given was something they were not ready for. They got bored and fought and they bred. The morality of it comes into question in deciding to try to put the genie back in the bottle by stopping them from breeding.
Then there's freedom vs. control. No this was not a recurrent theme because it was also a rejected idea. Even TIM rejected it for Shepard. He didn't want to control Shepard because he wanted Shepard to be Shepard. It wasn't about freedom so much as it was about remaining true to oneself. Control was seen as changing the person, not taking freedom away per se, but it made people react and be different. That's what indoctrination (extreme control) did. People were changed and ultimately died because of control. They all reached a state, a point where the dichotomy was too great to ignore and overcome. Benezia was fighting control because it had changed her-she became herself again before dying. Saren is actually seen to be figthing it-he had some actually good motives at one time perhaps but indoctrination had changed him. At last the division within him of who he was and who he had become was too great-he has realization at last and so he kills himself. TIM is kind of the same but he takes more convincing. He does have this realization too but he may force you to kill him. It isn't about freedom-it's about people being themselves. Under control, they are not.
The themes that most often resonate are unity, diversity, self-determination and autonomy (there's your freedom), and redemption. These are the parts of this character-driven story. And in such stories, heroes must be bigger than life and so must the bad guys-the reapers were, until the kid got a hold of them.