Why choose the Destroy ending over the others though? None of the endings leave us with a clean ending.
In Destroy all AIs are destroyed leaving no Geth, which, depending on your choices could negatively affect the Quarians
In Synthesis everyone is still alive, but part AI, part biological
In Control there are still Reapers running around and there is a Reaper Shepard.
I think that destroy would result in the most interesting scenario for a new game, personally.
Judging by the epilogues, in Control, ShepAIGod makes us all play nice. In synthesis everyone just plays nice because ... well, don't ask me why, they just do for whatever reason.
Destroy however, basically sets us up for an interesting new situation where the future of the galaxy is really unsure. The war is won but everybody lost a great deal. The galaxy is in shamble and needs to be rebuilt and re-ordered. I'd love to see how that plays out. Plus, Hackett's epilogue is much more ominous in terms of what is actually going to happen exactly than the other two, which are more long term specific.
Therefore, I think if they were to cannonize one ending, I'd go with destroy.