Not that Im in favor of how the ending went down but there are some things that I interpreted differently.
1. All the hate negativity over the god boy, am I the only one that thought that he was some entity (be it synthetic, synthesized, highly evolved organic) without a physical form so he manifested himself from an image that was ingrained into Shepards mind?
2. The cycle premise not making sence I may be mixing up with what the ending was and all the fan endings and debates I read. The way I see the cycle is that an ancient race made synthetic lifeforms (like the Geth) and were forced into war and to destroy them. Knowing that ultimately synthetic and organic life cannot coexist and synthetic life being better (virtual immortal, nearly infinite growth potential) that eventually synthetic life would destroy ALL organic life (advanced to simple).
To prevent that from occurring they created/ascended into the reapers which are actually synthesized beings. Leaving behind the citadel and relay network so all future advanced species would naturally expand along a known path. Every 50k years they come back and harvest the advanced species before they can cause irreparable harm to the universe by creating synthetic life. When they are harvested and help them become part of the reapers (think of it like the many hundreds of Geth minds in Legion). They leave the fledgling species alone to progress normally until they too are a danger to ALL organic life and the cycle repeats.
3. The Normandy scene I agree is the most confusing not sure why they are running away. As for your squadmates being there maybe I didnt look around during the race to the beam but I didnt see them, besides after you hit you hear them saying it was a failure and to fall back and regroup maybe thats what they did?
4. The relays were destroyed just as the being said they would, they were part of the reaper design and to mess with that design would break the system. Also without the crutch of the relays each species would have to develop at their own pace and not make quantum leap progress due to discovering functioning alien technology.
5. As for stranded starving aliens left behind after the assault I will give you that the stranded bit sucks but I imagine most thought they were going to die anyway. As for starving I would imagine existing food processing\technology would provide for those left behind. Its feasible to believe that human food could be modified in such a way that it was non-toxic to other races, at the time of the game it was likely just impractical given the ease of moving around cargo with the relay network but with real need Im sure it could have been done.
The thing is though everything at the end forces massive speculation on pretty much everything. There is no closure as the developers said there would be. Up until the end there seemed to be closure and clarity but it was all thrown out with the ending with some star child that comes out of left field. They said the end would not be like lost but it is in a way.
All through the series we have Shepard who is going to stop and destroy the reapers, nothing they say can change his mind. All of sudden this genocidal star child pops up and Shepard buys everything he says. So unlike Shepard. Also the Geth were not trying to destroy organics, they wanted to live in peace. But here comes the reapers to convince some of them to help wipe out organics. The ending is very poorly written compared to the rest of the game. This is why people are upset.