I finished it last night, and I have to say, I was conflicted by the endings.
The results themselves, well, they sort of make sense. The previous cycle was to destroy all advanced civilization to prevent the growth and spread of mechanical life, which would result in the permanent destruction of all organic life, ever, period. Allowing the primitive species to exist and evolve allowed organic life to continue. However with what Shepard did, it was obvious that organic life had reached a point of evolution and technological advancement that this cycle was no longer viable.
Command and Destroy endings were basically just resets on the ENTIRE cycle, bringing almost all galactic civilization back to square 1. Forcing them to rebuild the relays, the citadel, all that jazz. It was basically just a MUCH longer reset on the cycle, which will eventually settle back into what it was.
Synthesis ending made the least amount of sense, and involved the biggest stretch of the imagination. That signal somehow rewrote all DNA of everything, everywhere in the galaxy? Yea, space magic on that one. But, it was said that was the pinnacle of evolution, and the eventual path of all things. So sounded like synthesis was the only option to permanently and forever end the cycle.
Personally, I was disappointed by the endings. There was basically no variety, and a LITTLE more closure beyond "oh hey the normandy crashed on some planet somewhere, some people survived long enough to make a civilization that may or may not have any technology" for every single ending variation.
Sure, I can infer a lot of information on my own about how things might have turned out, but then it just comes down to, ok, geth and quarian resolution based on what i decided, they are locked in their own system without relays...........
krogans are no issue for anyone, genophage or not, locked in their own system, rachni, living or dead, no issue for anyone, turians, asari and humans all spend the next millenium or so recovering, then stay locked in their system,
salarians, they didnt get hit too hard, but again, locked in their own system, and worse, theyve brought the yahg to their planet which is now running loose.
Theres really not much more I can say, great great game, really bad endings. Sure, you can make some sense and get some closure out of them, but they could, and damn well should, have been better. Still worth playing.