You'd choose Control over Destroy if you felt that the potential risk of keeping the Reapers around was worth saving many lives. Not just synthetic ones, but organic ones, too: with the Reapers around, Shepard-AI can rebuild the relays quickly to get the galactic supply line back up and running to places that can't support themselves like Omega.
The issue with Control, besides the obvious risks associated with keeping the Reapers around, is that you have to trust the word of the A.I. controlling the Reapers that everything will work out just peachy, if only you kill yourself first.
From an in universe perspective Shepard choosing any option where the Reapers' master tells him or her to commit suicide, just doesn't make sense. It is one of many reasons why the endings to the series were poorly written.





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