Except an emp is disruptive to all technology. Again it's the computer vs calculator thing. And then there are cyborgs with implants in their brains and nervous systems.
No, I'm not over-analyzing it. This is a choice that affects the structure of the galaxy. Why I would choose this option has to make sense. Shepard would have to know that this new Catalyst won't start the whole thing all over again. Or do something worse.
And logic goes screwy when emotions are involved. Which can screw up the data its's receiving.
Except we know the Catalyst has been fudging the data. In at least two cycles it has interfered with synthetics to create a self-fulfilling prophecy.
And if parts of an argument that justifies galactic genocide are called into question, yes it's worth questioning the whole thing.
Some I agree with: Order vs chaos, victory through sacrifice, Surviving against the odds.
Organics vs synthetics, however is a peripheral theme at best. It goes largely ignored through the trilogy, and then is only mentioned in regards to the geth.
Similarly "whatever it takes" is only shown as a possible path. I'd say the theme is more "what are you willing to pay for victory?"
No, now it's a case of you making the informal fallacy of drawing the line wanting too specific of an answer and rejecting any that aren't 'precise' enough for you. You're arguing from incredulity now.
I don't know (or care at this point) how technical you think the scenario should be. It is, and it's not going to change. Let's put it this way; the tech is so advanced that we don't have a good way to explain it. You reject that, because you want the ending to make sense in such a manner that the applied setting is invalid so you can feel good about yourself.
And yes, you absolutely are overanalyzing it. You're rejecting any argument or statement or explanation as imprecise out of the hope that you have some means of watching your hero dance over the Reapers corpses with Ashley and friends. There's no explanation that works because you don't want it to work. As I said before, how the hell should I know how the tech works? You took the risk by building the Crucible, and now you're stewing around to question what it does when absolutely no one, not even the best scientists in the galaxy, have any clue? All you're doing is demanding an answer while rejecting any that might fit. You don't want an answer so much as you want to be right. Which, you're not.
Which is why no emotions are taken in. Thought patterns? Maybe. I'm sure a sophisticated, hyper advanced intelligence with over a billion years of history and data to look over can detect the issues with emotions and thought patterns. Maybe your Shepard is psychologically broken and screwed up. Mine isn't. He's as rock solid and chill as ever. Now this is an appeal to emotion where it might not exist for a Shepard.
We don't know how or why or even if the Catalyst has been at all responsible for the data. You're being awfully presumptuous to know the context and meaning of events, technology, and the nature of the Reapers where we've been given almost no information whatsoever. So I call this point into question on relevance. You're making a formal conclusion to a very limited set of inductive answers. Nice to know you know everything. If that was the case, why couldn't you find a way to beat the Reapers conventionally?
Negative, that's not how arguments work. That's actually a fallacy fallacy; you're assuming that since a claim is argued poorly and that a fallacy exists, the entire argument of the Catalyst is wrong. Which is a fallacy.
And no, it's a pretty central theme: hell, you fighting the Reapers proves it. Not just the Geth. As well, you're incorrect in stating that order vs chaos is prominent while synthetic vs organic is not. As it's presented, the latter theme is unanimous with the former theme.
As well, whatever it takes to victory is a theme. Your question has an answer; my theme. Your answer was proven wrong by the ending. By the Reapers. Thus, by the very central theme.