Destroy all the way.
Put yourself in Shepard's boots for a moment, rather than thinking it about like the a player who knows that a sequel will never have any of the three ending choices result in mass extinction. Would you trust the megalomaniacal A.I. and his fleet of thousands of mass-murdering machines, responsible for the mass extinctions of perhaps thousands of sapients species, to embrace peace and protect galactic civilization rather than destroy it?
I don't know about you, but in Shepard's boots I'd shoot the f-king tube before Glow Boy finished a single sentence.
I do wish there were a "I delete data like you on the way to real errors" option just before choosing Destroy.
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I choose Control or Destroy. I like the potential of "Control". The AI concept is more versatile. In my headcanon, Reaper-Shepard-AI spends years rebuilding what was destroyed, but gradually purges her human memories in favor of heightened system processing, becoming more and more of the machine that made the Reapers. In her last moments as a Reaper, she holds on to the memories of her LI and uses that as final incentive to send the fleets flying into the sun. The purged data winds up in the Citadel, which then forms a new AI that protects the Citadel, but has no data or memory of her old lover (and continues to search tragically for the missing pieces!)
So... still dead, still sad love story, but being an AI in the Citadel feels more right than being in a Reaper, at least.
I'd like to think her function there is harmless, similar to the Keepers. To maintain and protect it. Perhaps a bit more evolved to protect the inhabitants as well.
More importantly, I just want the potential to meet EDI again in the future to have nice AI talks and exchanging-of-data. I'm sure there's flaws to this headcanon. *sob*