I think I may have finally figured out what Bioware was thinking with the ending. I know lots of people must be tired of the ending debate but hear this post out it is a little different.
MA is a love letter in many respects to science fiction. One can easily find half a dozen nods to other science fiction stories in Mass Effect (MA). It makes sense then that the ending of MA would be the same and I believe it is. The ending to MA 3 to me feels like a combination of the ending of Battle Star Galactica(BSG) and Babylon Five(B5). More B5 then BSG. If you have not watched B5 you will not know what I'm talking about and should read or watch how season 4 ends to understand. B5 like MA is all about an endless cycle. In B5 two old races the Shadows and the Vorlons control the cycles one representing chaos the Shadows and the other order the Vorlons. I believe that the MA writing team used the same concept except they combined the two races of B5 into one race the reapers.
When I say the reapers one thinks of the giant squid like mile long killing machines, but this is just one side of the reapers they have two sides to them. The Citadel and all the mass relays are in fact just as much reapers as are the killing mile long ships. Both work together to create the cycle. The Catalyst(the head reaper) says it himself, he is the Citadel. It took me time to process what that all means. If you think about it that beautiful space station that most MA fans love is a reaper just the other side of the reapers. The Citadel and the mass relays are the order part of the reapers plan it control the galaxy or in MA terms the Paragon side.
I think this is a good ending and puts a different spin on all three games and makes you look at it in a whole new light. That said the MA writers did not flesh it out enough they don't make this fact clear to the players and mess it up. They should have had Shepherd voice out this revelation in-game. That revelation being that the Citadel and the mass relays are not just reaper tech they are 50% of what and who the reapers are and what they what to do. In short the mass relays in a way are as responsible for the death of galactic civilization as the squids.
I stress this point because many people hate the idea of the mass relays blowing up but the truth is without them blowing up you don't defeat the reapers. The reapers and the relays are one. To break free one must destroy the whole system. the giant reaper killing machines are just part of the whole machine. The other part is the relays. Its all about control the reapers use much more than just Indoctrination to control their greatest form of control is the relays. The Citadel and the relays are the order part of the reapers. They may look nicer than the war machines but just as deadly and controlling in the end.
Again the writers don't flesh this all out and that's where they fail. It kind of clicked for me when I heard the reapers talking about order and controlling chaos. That is what B5 is all about. It all makes sense but its not nearly as clear as it should of been and that's what I think went wrong. The other problem is the reapers reasoning. Instead of sticking with B5 they only give one concrete reason that is to stop synthetics from destroying organics. That is one reason yes but their are several more ways organic life can produces destructive chaos such as messing around with other organics like they did with the Krogon or explore to fast such as with the Rachni or try to evolve to fast such as Cerberus. The writers should of had the Catalysis list those reasons as well. If any one wants to talk I would love to talk about the reasons for chaos the MA universe gives us.
I'm 90% sure this is what the writers were trying to convey they just did not convey it very well, that's why I think the DLC should make the ending better. To know what would happen if anything of the reapers were to remain such as the relays just watch season 5 of B5. That seasons shows what happens if any mechanism of control remains. Hint not well.