If you made peace or destroyed the Geth, that story arc was pretty much resolved.
You can argue that it doesn't make it THE theme, but by the basics of narrative structure, making the organic-synthetic conflict the motivation of the Reapers automatically ascribes more thematic relevance to it than the other themes. Keeping the Reaper motivation more general like in the example I mentioned allows each of the major arcs to contribute on an equal level.
Very well said. The bolded actually encompasses my strongest criticism against the ending. The Catalyst's focus on Synthetic-Organic conflict elevates certain aspects of the narrative which, up until this point, had encompassed a sub-plot at best. Suddenly, Rannoch has higher importance/priority than Tuchanka or Thessia.
The best, most complete ending would have done its best to make the Catalyst's motivation touch on everything the player had experienced up until this point. This is why I've argued that the Reapers' motive should not have been Synthetic Organic conflict, but simply conflict in general. Given sufficient time, it's possible for a species to acquire such advanced weaponry that it will cause massive destruction. It's something applicable to every moment in the game (since the player is always killing something it can function as a meta-commentary on the nature of games) and has a fair bit of arguments to support it. Hell, during the Cold War we were worried about nuclear weapons destroying our planet. Now imagine if even more advanced species got there hands on something similar.
I don't need proof of everlasting peace between Synthetics and Organics. I just need proof that peace in general is possible. Just as it's possible to have beace between organic races. We are none of us slaves to destiny. And that is where the Catalyst is wrong. Wrong. WRONG!
Also this. ME2 and 3 go out of their way to deconstruct the notion that there is a fundamental difference between Organics and Synthetics. On that basis, there's no reason to fear Synthetic vs Organic conflicts any more than Synthetic vs Synthetic or Organic vs Organic.