Isn't it sort of the case of "You can only have one first impression"? Meaning you already have your ending, how can you really change it now and have it seem right? Patrick Duffy makes an appearance and dreamnt it all?
The ending should have been, they stopped the synthetics killing the organics in whole. Then have a Jacob's Ladder type of ending where you zoom out to a larger picture and Shepard (ordinary joe) is on a operating table, the DR. says; "we tried everything but we couldn't stop the cancer from spreading". Meaning the organics were really a disease, but a disease never looks at itself at one, the synthetics were the cure. Or maybe not.
But any and all endings now are way too late to consider now. The game has shipped with it's ending.