So I just beat the game again (only for the second time, though). My God, how can anyone ever choose anything but Destroy? I don't even care that you supposedly kill EDI and the geth that way. It's far easier to ignore that and enjoy the rest of the ending than it is to choose an ending you don't want just because of some stupid BS complication BioWare added so that people would choose their "ideal" ending.
The only other time I'll choose something different is with my pure Renegade, who'll pick Control and rule the galaxy!
Although I do still favour destroy (and I agree is "drawback" is bollocks), I really wish the EC would have shown the consequences to the other synthetics. A brief scene where EDI drops dead as the wave hits and just slumps over in the co-pilot seat right next to Joker would have worked. Some shots of Geth platforms dropping dead should have been in there too.