For anyone who wanted Lenny and George to actually find peace and happiness, yeah, it's a bad ending. But one doesn't read Steinbeck for "good endings"
And it would be even worse if "Of Mice and Men" was an interactive narrative that claimed that your choices affected the outcome.
Which is why I say Destroy's killing of all synthetics everywhere is both inexplicable and arbitrary: a punishment directed at the player for daring to not pick Synthesis, or at least Control (you notice Destroy is also the only ending with a Low-EMS, "Earth is a cinder" outcome as well).
Achievement unlocked: failing to answer a rhetorical question. 
You said it, one does not read Steinbeck for a happy ending and it’s the same with ME3, if you think this can end well, you didn’t pay attention through the game. Or you only saw what you wanted to see. ME3 is one giant farewell drink and I’m not even talking about London.
I understand your point when you use the word punishment, though I don’t agree at all. The destruction of all synthetics makes perfect sense to me. This ending needed a downside, that’s how dilemmas work (escape hatch, blah blah blah). The threat of AI rising again is not important enough and barely works as a sword of Damocles. Besides this threat is also present in the control ending since Shepard’s AI might blow a fuse and start a new harvest. Lore-wise, I consider the red beam as a sophisticated EMP that targets and fries the most advanced electronic and computer hardware. The more complex the circuit, the more fragile it is, especially regarding electromagnetic fields. Or it can be something so complex we don’t actually understand, call it space magic if you want but remember Clarke’s law: Any sufficiently advanced technology is indistinguishable from magic.
While I don't disagree here, the difference is that Georges was a character defined by the writer. Shepard was supposed to be a character designed by the player - don't make me go to Youtube and find the videos. "You are Commander Shepard." - Casey Hudson.
We didn't find out about the purpose of the reapers until the last five minutes of the story. There was no foreshadowing. It was totally arbitrary. Yeah, that Rannoch reaper talked, but I mean who really cared about what it said. We were at war for our survival. Who cares about order and chaos? The last five minutes. That is not the time. Forget Leviathan because 90% of the people who played the game didn't play Leviathan. I haven't played it yet, and I have the DLC.
The ending is controversial, and will remain so. I hope Bioware never does an ending like it again.
I won’t talk about choices, rails and freedom in video games, this is way off topic; but you should play The Stanley Parable (It’s a bit expensive but you can easily find it for 5 bucks during Steam Sales. You might learn something about how choices work and why freedom doesn’t exist in video games).
Mass Effect is a RPG. It doesn’t mean the player can do whatever he wants, it means the player can do whatever the character can do. You may think BioWare force us to choose their own endings but (in my opinion) it works because the catalyst forces Shepard to choose too. So yes I can’t create my own ending but neither does Shepard. We are Shepard doesn’t mean Shepard is an omniscient-omnipotent human. I don’t mind if I can’t change the outcomes as long as the character is in the same situation (Catalyst, Virmire) On the other hand, some choices are poorly handled and it happens when Shepard takes the initiative. In those situations, Shepard can choose freely but in the meantime, the game forces a choice with limited outcomes to the player (ie : Racnhi Queen and Shiala, I wanted to keep her in custody and let the council decide ; Legion I wanted to destroy/dismantle it ; Collector Base : I wanted to give it to the alliance) You are Shepard =/= you can shape every detail of the world.
And we didn’t find out the purpose of the collectors until the last five minutes. And we didn’t find out the purpose of Sovereign at all. AI has always been a part the story, much more than the dark energy thingy. The problem with the plot-twist is that Ranoch thematically resolved the confilct between organics and synthetics (I don’t remember who wrote that but I like the idea) so it’s kind of weird to hear about that again at the end.
Of course the ending is controversial, I don’t deny it, tough I think it didn’t deserve a 5h1tstorm like that because it could have been way way worse. I played Call of Chtulhu RPG long enough to know that messing with god-like creatures (and Reapers are very Lovecraft-esque) usually lead to painful death or insanity if not both. I also was a fan of Fallout and then I played Fallout 3
so, frankly, we should be grateful.