Ultimately the problem is that they didn't really plan (or EA takeover derailed the plan). ME2 should have laid the groundwork for what the reaper stood for (theme) but also how to defeat them (in a way that would resonate with the theme). But instead, it spend almost all of its time introducing a new crew... just to discard them all in ME3. As much as I like ME2 (gameplay, character), it really feel like a side chapter that should have been more of a ME1.5 while the real ME2 was cooking. It'll never happen, but I would so love a ME remake that would do just that.
So ME3 just didn't have the proper time to get around to create a theme in just one game... but they still didn't try and instead most of the overarching plot of ME3 is spent dealing with Cerberus and Kai Leng, which doesn't feed at all into the organic V synthetic things. Its more about control... or something?
I'm putting most of the blame on the way ME3 was rushed through development. There is probably a way to make the organic v synthetic conflict seem more thematically appropriate, or there could have been another direction altogether, but it being a really stressful production probably did a lot of damage to the writing. I did look up an article on what might have been Drew Karpyshyn's ending, but he himself admitted that it was never really fleshed out in detail, and per his words, "just as likely to disappoint".
You mention Cerberus and the seeming theme of control, but IMO there's another far more interesting angle they could have gone with: what if Cerberus/the Illusive Man had started advocating for synthesis instead? They had the funding, willingness, and by the end of ME2 access to tech no one else in the galaxy did. Since the Illusive Man's whole thing is furthering humanity's interests before everything else, maybe he could have become indoctrinated to believe not that he could control the Reapers, but that he could spare humanity by advancing their evolution into a new form of life? That would be both in character and much more compelling than his saturday cartoon villain speeches about controlling the Reapers. Since humanity would have become both organic and synthetic, you can see how they might fall outside of the Reapers' stated goals, right?
It would also have been a spin on the fate of the Protheans turned Collectors: they were enslaved by the Reapers by getting captured and forcibly changed, LOTR Orc style. Humanity under an indoctrinated TIM would have become servants of the Reapers, but
willlingly, believing they were ascending to a new form of life, but ending up as slaves. That way the synthesis ending would probably have carried a lot more dramatic weight and moral complexity than being a catch-all feel good ending. It would also have made Shepard acting under his own will much more impactful, since organic life ascending to synthesis on their own terms would leave the galaxy much more open to possibilities.
I also straight up started another playthrough already, this time on Insanity as a full paragon Soldier maleshep. I've never actually played the Soldier class, so I'll finally get to use all those assault rifles in the games. I added some quality of life and graphics mods (skip the decryption minigame, unlimited sprint, removed camera shake, readjusted lighting and galaxy map tracking for each quest), and jesus fucking christ they make ME1 so much better. The unlimited sprint, while probably seriously messing with how the game's balanced, makes traversal so much faster it's insane. It does lead to a rather funny scenario where Shepard and his squad are bolting down the hallways of the Presidium on errands, weapons in hand. Skipping most of the dialogue also cuts out
so much from the playtime. Insanity is where I finally feel like I have to actually pay full attention to the game, consider each level up and party comp. It's still not very hard, but definitely more fun than on lower difficulties.
