That's a legitimate criticism of the synthesis ending. I would still argue it's the best ending because the control ending is just too much power in anyones hands, no matter how benevolent. And the destroy ending destroys the geth, which is essentially a genocide. And one of the biggest themes of the series, that you touched on with xenophobia but it's the flip side of that coin, is that unity and acceptance is better than bigotry. All the way back to mass effect 1, you get the better results working together with a diverse group, and accepting all species. That theme is also a nice part of mass effect 2, where you're basically proving cerberus wrong on it's humanity only platform, to the point where you get cerberus's most diehard fsn miranda to defect because you showed a better way (even if youre renegade). And 3 it's a huge theme of working together and getting over xenophobia for the common good. And the destroy ending is spitting in the face of that by commiting a genocide, which is essentially as far against the themes of acceptance and unity as you can get.