... Love the discussion going on here!
As it happens, I'm working on a post-ME3 piece following my canon, so I've had to establish the setting and details of a post-Sync galaxy very clearly. It was something I tried and failed in the past, but am trying again with a better vision of what kind of world this is going to be, and the writing has been coming along very nicely this time. I might even share it!
Anyway, here is my vision of the setting: ...
1.) Workings.
Though retconning the ending with my revised version of the same thing was tempting, I ultimately decided to keep it canon-compliant, for a host of reasons. So, the implementation -- problematic as it may be -- stays.
Initial effect: for organics, nothing. All anyone knows at first is that they have funny green tattoos now, but have no idea how they work. The Reapers, however, are liberated -- totally free of control and now autonomous. I actually believe this was the Catalyst's hope for them all along, that at some point an optimal solution would be found where they would take some place in society, and so the sacrifices made to preserve every civilization was not for nothing.
Given freedom, the Reapers have no real motive for conflict. No Reapers (not one!) continues previous aggression. Once their side of the story is made clear, some tentative support is given to them to help rebuild the galaxy. Again, they're not without critics and bitter enemies, but those elements ultimately don't matter in the big scheme of things.
Understanding: to understand the changes that took place, it proves necessary to have knowledgeable technicians and experts on synthetic tech; new abilities of organic life are "unlocked" with research and study. Those with AI assistance in their research have much more success than others. While the rest of the galaxy is slow to trust AI, the few species with some experience there ultimately lead the charge: humanity (courtesy EDI), the quarians (courtesy geth), and salarians (only race quickly willing to accept AI assistance, including the Reapers').
However, the Council ban on AI creation is eventually lifted when it's clear no one will follow it.
Breakthrough: what's learned is that organics (if willing) can establish mental connectivity with any devices capable of handling such a connection (chiefly: omnitools, computer-terminals, VI hosts, and even AI lifeforms). In doing so, they can acquire the capabilities of any devices they are linked to, on a mental level. In sync with an omnitool, you can take in all of its functions as your own: calculators, exact time, maps, what have you... any ability once thought exclusive to AI is now possible for organics. The more advanced the device, the greater the benefits. Organics can also remotely-control things like mechs and drones to serve the purpose of carrying out dangerous and laborious work.
This connectivity is made possible by nanotechnology, spread by the Crucible and received by organic lifeforms, coordinating the nervous system (brain) with external devices. It initially affects all organic life, but the effect wears off of lifeforms that do not actively use it -- flora and fauna eventually see the change go dormant and return to mundane form.
For synthetics, the ability to learn about organics is made easier. They can do it in a way they are most comfortable with: memory-sharing. In establishing trust and safety with organics, synthetics are more inclined to cooperation.
Cyperspace: perhaps the biggest change here is bridging the gap between the "real world" and cyberspace. While connected to some device, part of the organic mind can work in cyberspace, where data can be shared in a fraction of the time it is done in real-space. This is one huge area where the difference between organic and synthetic is eroded, and why the Catalyst may feel like his work is done: synthetics can no longer universally out-think organic life.
Name: since the term "Synthesis" is only used in the decision-chamber, civilizations come up with their own name for this phenomena. Humanity calls it "Harmonics," likening it to biotics, but working through tech rather than eezo. It also aptly describes the nature of organic-synthetic relations in this world -- conflict yields no benefits, only cooperation does.
2.) Controversy.
Perhaps the biggest issue with this ending as it exists now. This is addressed near the beginning of chapter one. It's established that not everyone's happy; there's some opposition to how this solution was enacted. It is what it is.
Some accommodations are made for these opponents, though. Groups of people choose never to make use of these abilities, and thereby proceed to live their lives as normal, "off the grid." Since non-sapient organic lifeforms have seen the effect wear off, it is thought that the same will eventually happen for those that shun the change.
Additionally, radiation treatment is developed to "kill" the implanted nanotech, permanently and immediately doing away with the effects. However, no one of note in my story is un-synthesized. It's just not practical, only visceral reaction.
3.) War and Peace.
With breakthroughs across the galaxy aided by the Reapers' high processing-power, it becomes much easier to solve problems through innovation rather than war, and so the deep-seeded issues that typically cause these conflicts are dealt with swiftly and preemptively. As such, you see the "Pax Galaxia" as EDI's epilogue-narration indicates.
However, "peace" in this context simply refers to the absence/obsolescence of major, galaxy-scale conflicts. No major war stories will take place in this setting. However, small-scale, localized conflicts will exist as always -- it's simply natural. In truth, these conflicts may actually be more interesting to explore (as were most non-plot missions through Mass Effect).
I think some potential plotlines you could see out of this setting would be things like: (1) space-exploration, venturing to uncharted planets; (2) cyberpunk plotlines, big cities that have not yet felt the benefits of galactic prosperity for one reason or another, and all the conflicts that come with life in major metropolitan areas with both the super-rich and dirt-poor; (3) abuses of technological advancement, through corrupt or otherwise irresponsible organizations. Some experiments gone awry or competitions between rival groups vying for some kind of power.
I don't see BioWare taking the next title in this direction. That's okay: I'll use these ideas for my own stories.