Before I comment on this, let's make one thing perfectly clear: ALL of the "choices" given are railroaded abominations, extremely reprehensible in terms of morality, and not a fitting ending to Shepard's epic quest at all.
Now, what makes "Destroy" the least abominable stinker out of the original three choices?
For starters, it's the most thematically consistent with Shepard's journey, even if it fails to convey a clear sense of victory over the civilization-devouring horrors from dark space and has their gestalt-overlord basically hand you the self-destruct trigger on a golden platter.
But let's take a look at your objections.
CosmicGnosis wrote...
- Kills synthetics; prevents synthetics from continuing their quest for personhood
Arguing in-game, this happens for no good reason whatsoever.
Arguing on the meta-level of storytelling, it's clear that this massive drawback was added by Casey and Mac because they did not want people to choose "destroy" - they clearly want you to regard Synthesis as the Golden Solution, the Big Prize you have to work the hardest for.
Nevertheless, the Synthesis solution is so ill-written, hackneyed, implausible and morally problematic that it does not really qualify as an alternative.
The galaxy is prejudiced again synthetic intelligences; choosing Destroy does nothing to challenge this prejudice
In-game, there's no reason why the geth-quarian peace should not permanently change the synthetics' place within the galactic framework of civilizations. But that's not what Mac and Casey introduced as the Big Conflict to begin with. Their ultimate bogeyman introduced in the final five minutes was a monster we have never actually seen: a post-singularity AI that has basically outpaced organic evolution so much that it'd be safe to call it "divine". A being so exalted that it'd regard all other sapient life as little more than vermin polluting the galaxy, as far removed from itself as germs are from us.
Depending on EMS, it either destroys or damages technology; even if technology is merely damaged, there is a cleaner way to end the cycle (Control)
Becoming Space Dictator violates everything that Shepard is and stands for. Regardless of whether you play cosmic policeman (Paragon) or tyrant (Renegade).
Throws away the knowledge contained within the Reapers; in my opinion, conquering the Lovecraftian entities means understanding them, not killing them and treating them as mysterious, unknowable monsters
Control does not signify defeating the Reapers - it means JOINING them (even if you change their agenda), BECOMING them. Not an option.