Im sorry but you don't give enough, nor good, arguments to defend the ending. You're just saying "it's good cause it's good". I read your article, and it's vague and doesn't seem to have any thought on it. This is the impression I get from reading it, that you're just saying "Great" to be on the opposite side, everyone loves to be a rebel.
But the defense "You can't save everyone" doesn't apply here, since you save no one. It's true, it's a war, you can't save everyone. So the final decision is basically kill everyone, that does not make sense. And what you fail to see is that the final decision is not your own, but one that is imposed to you, by a being with god complex with a really flawed logic that forces you to choose between three colors.
If you think that's great, by all means, please, continue being happy. But for the rest of us, it's called ignorance, and willful ignorance is a synonym of stupidity (and sorry for the wording, there's no other). If you are just being a conformist about the ending, alright, but don't try to defend it by using your own conformism because people is going to jump on you with actual logic and well thought-on arguments that you won't be able to rebate.
Plus, no, by basically 1. wiping all life from the galaxy 2. leaving it in a dark age you negate all the choices and efforts done in ME1, 2 and the rest of 3. So no, your choices did not matter in the end. You cured the genophage? Great I hope they can enjoy it while they can. You unified the geth and the quarians? Absolutely fantastic, pretty much all the quarians are stranded in Sol System and won't be able to see their homeworlds, that they finally retook, in quite a few generations (aka never because the liveships won't last long enough). Do I really need to continue? Because Palaven is also quite ****ed, and Krogans are stranded there as well.
Just saying, if you want to keep loving the endings, remain ignorant.