But the way you resolved the other main plot is. Because if you chose the Geth or brokered peace then that decision is rendered moot by the Destroy ending because it also magically kills all the Geth. (Not to mention that the fact that a peace option even exists completely undermines the alleged motivation of the Reapers.)
And if the Krogan are rewritten into new part-synthetic organisms does the genophage even still work? So does it matter what we did there, because even if it was immediate genocide on Tuchanka there are enough Krogan not there that it wouldn't matter.
The endings as presented have concepts in which break and devalue the other side stories.