They were both arbitrary and illogical
shoot tube, make all AI die. Regardless of origin. But other tech? A-OK!
Oh, and walk into the explosion while you're at it. Because feelz
Grab control rods, overwrite AI. Forget that it wasn't made for a human mind, was likely designed before there even were humans. And fry. Because reasons. And don't worry, this AI Shepard will totally act like Shepard, despite all that stuff about synthetics and organics being destined for conflict. Everything will be A-OK! Probably.
Synthesis: Let's achieve the "final evolution of life" by the power of Shepard leaping into the space magic.
And that's not even going into the Catalyst's insane troll logic.
And yes, themes need to be consistent. Perspective doesn't have to be. You can look at things from other points of view. but without internal consistency, all you've got is a lot of stuff happening.
Though yes, what you do could have affected the Crucible: What kind of resources and personnel you have working on it, which would affect what it was capable of. Though frankly I would have preferred something other than "we found this blueprint to a deus ex machina in the 'small data cache' we've known about for decades and just didn't turn up until right now"
Those seem more like issues with the execution than actual issues with what's presented. Thus speaking, you're saying nothing against the ending that isn't technical.
Destroy makes the most sense (even if shooting a pipe is a weird way to activate something): It targets the energy systems of synthetic systems, releasing a radiation burst that kills synthetics (or destroys higher processing powers which would effectively do the same thing). Of course, it's speculation, but it does make sense.
I can't explain the walking into the explosion part. Yeah, that's bad. That's technical. Falls under execution. I've never denied the endings were poorly executed for the most part. But that doesn't mean that they were bad or inconsistent in any way. Just poorly portrayed.
And yes, Shepard probably has his brain scanned, and had the new model built on those blue-prints. Makes sense. It has his memories and thoughts, while getting rid of his feelings and emotions. Makes sense. It overrides the software (if not the hardware) of the Catalyst and replaces it with a new mandate created by a new personality. The Catalyst is now a facsimile of Shepard, including his thought patterns and memories. Not hard to understand at all if you try. As I said, execution was iffy, but that falls under technical design issues.
And yeah, the implementation of Synthesis is bunk. The concept behind it is still fairly sound.
And the Catalyst doesn't really have insane troll logic. Maybe a gap as far as how it defines the term 'synthetic', but ultimately, its perspective is sound. You not understanding or refusing to understand it does not make it troll logic.
No, they don't need to be consistent. And you're defining internal consistency as the same thing as a theme. Internal consistency is logic, lore, technology, dating, events, things that make up the universe setting, not themes. You're saying inconsistent things that have nothing to do with themes. And the ending deciding to create a new issue and a new theme doesn't change or negate the previous ones (well, mine at least).
You winning morally and heroically and by the rules is not part of the lore, nor is there any obligation for the lore or the Reapers or the Catalyst or Bioware to abide by your perspective.
Nobody - nobody - knew what the Crucible was capable of. That doesn't make sense to have people know what it does.
And yes, it would have been better to have some foreshadowing and background to the Crucible. But again, that falls under narrative and technical execution, not thematic dissonance.
You haven't said anything substantial at all.