Still, Legion's choice runs contrary to his own stated view point in ME2 where he exposed the importance of each species, including the geth, to evolve and develop at their own pace, in their own way, by their own means; i.e., self determination. Legion's final act could be seen as character development on his part, I suppose, though I wouldn't necessarily call it positive character development. His decision is one made at least partly out of desperation to avoid extinction and involved compromising his beliefs, so in that sense the only real difference between him and Saren is the self sacrifice bit, and complaints have been thrown at the game about how contrived that aspect of Legion's story is.
And the synthesis ending itself is still a case of it being forced on the galaxy. One person has a choice in this; no one else gets a say in whether they get matrix code skin or not. So it isn't synthesis by force vs willing sacrifice, it's forcing synthesis via willing, arbitrarily contrived sacrifice.
And you still have a lot of examples that run contrary to the synthesis message; Legion in ME2, as I said. Javik continuously speaks about how conforming to a single path is what doomed his cycle. Mordin's story arc and a lot of his philosophy, and really the salarians in general with their short sighted tendency to 'uplift' other races to solve immediate problems without thought to the long term consequences, which prove to be disastrous for all parties. That's essentially what synthesis is; forcibly uplifting every species in the galaxy whether they're ready for it or not.
Ugh. I've been up for about twenty minutes and haven't had any caffeine yet.
But everyone is also using their own justifications for this.
Uplifting the Krogan for example, is not the same as Synthesis because it was again, forced. Bakara also implies the Krogan were already in nuclear winter at this point, so their species was on decline. The Salarians own hubris as you say is true, but the entire arc runs parallel to what Saren did; the forced change without consequence.
Legion also should change as a character, and it was growth of the character from before. You basically had the choice of a genocide or evolution in that scenario as you say, but it was also something that Legion implied might be necessary for their long-term evolution. There is no going away from that; Legion felt the code was important enough to keep when others would say no, and Legion had ulterior motives for it early on, I would say. We also see Legion evolve throughout the game, witholding information from Shepard, talking about how his people are afraid and went back to the Reapers for preservation, and so forth. His own stated views changed, part of that may have been exposure as a platform to Shepard, Tali and so forth, part of that just the evolving thoughts of how people behave. Mordin is another example, his own justifications for the Genophange into a different direction this way. So characters staying stagnant is not a bad thing, it makes them believable as characters, and realistic in the context of the world.
The real crux of this is going to boil down to point of view, we both know that. To put it this way though, Legion as a character made the choice of self-sacrifice yes out of preservation, but also out of evolution. Legion wanted this for his people, because it knew that evolving was their only chance to overcome their own limitations. The real difference between Legion and Saren is not just self-sacrifice and motivation, but actual, evolving beliefs and how to achieve their desired goals. One is positive, one negative; both attempt to force evolution, but only one of them can work because they are not subjugated, they are not controlled, they made that choice.
Not to mention supporting Legion at this point more or less says Shepard is open to the idea of Synthesis in the long run; justifications for it don't matter, you are essentially allowing the Geth to rewrite their entire population, whether they like it or not. The issue will always boil down to it being an ethical one, but I never bought that the idea behind synthesis is a fully bad idea (it is an unknown idea that is presented as utopian, but it can have flaws like anything else) but it certainly never came out of nowhere. The game lays those seeds, the question is do you sow them?
I guess we can just chalk this up to an agree to disagree type of thing, but if nothing else once again the endings prove their worth in having an actual conversation.