Bioware have announced Mass Effect 3 Extended Cut which aims to clarify the ending. I've been thinking, how could they make sense of things? How can clarification bring closure? I was able to come up with something.
Let's assume that the events of the ending with the Illusive Man and the Star Child as well as the 3 choices are in fact real. Let's discard the Indoctrination Theory, hallucinations, dreams or any other "it wasn't real" theories and treat it as reality.
One of the things that baffled me about the Stargazer at the end was how could they not have space flight? Remember that the little kid asks when he can go to the stars and what will he find? Even though the Mass Relays were destroyed in all 3 endings there were still spaceships with "traditional" faster than light drives. Space travel should still possible, it just takes years to do instead of minutes now. It occurs to me, though, that the Stargazer is probably a descendant of somebody from the Normandy crew and that the world we see isn't Earth but rather that the idyllic garden world we see the Normandy crash land on. They wouldn't have space travel even though they have a broken ship. They wouldn't have the technology necessary to fabricate new or replacement parts. They are essentially a new society. It also would be extremely unlikely they would be found by the rest of the galaxy since traditional FTL is slow and that idyllic world could literally be anywhere in the known galaxy.
Before I go further let me delve into the topic of FTL drives and their speeds. It's said during the Arrival event
(after the destruction of the Alpha Relay) that they anticipate it will
take the reapers a year to reach the nearest Mass Relay and thus reach Earth. The reapers
were able to do it in 6 months implying their FTL is twice as fast as
the rest of the galaxy. The reapers went to somewhere else in batarian space so they didn't go far but one would assume it wasn't "the next star over". That means it is possible for FTL drives to travel significant distances in years. It's certainly not as fast as a Mass Relay but it is possible to travel around the galaxy if you have the time and supplies to do so.
So we've solved the pre-space-flight culture the Stargazer lives in and we have some idea of what can be achieved with traditional FTL speeds. What about the genocide of the quarian and turian races? The answer to this was actually staring at us all along but I didn't see it. The quarians brought their liveships to Earth. Those big ball shaped ships are liveships where the quarians produce most of their food. Assuming the reapers didn't destroy them then the quarians can provide food for both the turians and quarians. Since they can produce food on a ship the quarians only have to live long enough to travel most of the way across the galaxy from Earth back to Rannoch. Based on anecdotal evidence about how fast FTL speeds are it would take a few years but would be possible. The turian homeworld of Palaven is much closer to Earth so it would take them significantly less time. It's possible the quarians could provide them food or even an entire liveship. In either case, assuming some of the liveships survived the fight for Earth then the quarians and the turians can survive.
That leaves a few other races. The asari live long lives so they could easily make it back to Thessia. The only obstacle, really, is having enough - or being able to produce enough - food to make the journey. Surely they must be able to - or can retrofit - some of those huge ships they have to produce food for the journey. In my game there weren't many salarians at Earth and I don't recall Sur'Kesh being attacked so the salarians are probably fine. They lose some people but much less than other races. Also I don't think Sur'Kesh is that far away so the salarians could probably make it back home even with their short life spans. That just leaves the krogan. I'd imagine the turians could take the krogan home or at least most of the way. Food is, of course, an issue since they can't eat the same thing as turians. Still, though, Tuchanka isn't all that far away relatively speaking.
The above comments cover all 3 endings and how those races could survive. The only ending with a difference might be the Destroy/Red ending. In that ending the Star Child claims that all synthetics (the geth and EDI as well as the reapers) will be destroyed. The Star Child also heavily implies Shepard will die because of her synthetic implants. Except we see (with a high enough effective military strength) that Shepard does not in fact die (I still cannot offer an explanation of how Shepard takes her breath back on Earth, however). Could this also mean that the geth and EDI were not destroyed? Was it a lie or some type of falsehood by the Star Child meant to deter Shepard much like the implication of her own death?
So how is this better? Well it means Shepard didn't commit genocide on several races. Sure, the end result was the destruction of galactic civilization but it's possible to rebuild the Mass Relays in time (The protheans made the Conduit, after all). I think that the loss of the relays would still be considered a victory to end the reapers once and for all. It certainly sets the galaxy back several hundred years, though. I think the races would be able to rebuild the mass relays but first they would need to figure out how they worked and for that I think you would need the asari, salarians, quarians and humans (and probably the turians) working together which is now problematic.
So, what if these are the clarifications Bioware ends up making? Well it would be a great start, certainly. At least my Shepard wouldn't be a war criminal with the death of two or more races on her hands. It still doesn't explain why Liara (in my game) was on the Normandy when she was last seen with Shepard getting blasted by Harbinger. It also offers no explanation on how Tali or Garrus will survive on a garden world where they can't eat anything. I'm also unsure of the minimum number of people required to have enough genetic diversity to prevent extinction. It's possible the Normandy had enough people for that. That doesn't help Tali or Garrus though who presumably die without producing off-spring. In my game Liara and Shepard were a couple so that doesn't help her either. Liara would live for several more centuries, too, which presents other questions if indeed the Stargazer is a descendant of the Normandy crew.
If it turns out I'm partially right I think I might be okay with that. There are still a lot of questions that need answered even with my crazy talk above, though. Lots and lots of questions. It also doesn't get Liara and Shepard anywhere near each other so they can have the promised little blue babies but perhaps that's wishing for too much of a happy ending.
I guess we'll find out this summer.