Probably they did it so we have all these debates and theoris, making the game even more famous and leaving its mark in history.
That or EA was sick of it being delayed and just told them to hurry up and fucking ship it. Watched the extended cut endings on Youtube, they're definitely an improvement over what we had originally.
I am still wholly unsatisfied with their "clarification". The fact is, it is based on the idea that the only way to stop the machines rising up and destroying all organic life is to have a bunch of machines destroy most of organic life. It doesn't make any sense at all, and BioWare stuck to it. Other aspects do feel a bit better though. The Normandy leaving for example, and the crash landing stuff. Also they addressed what would happen to all the races now that the mass relays were destroyed. I am a huge fan of the indoctrination theory. I think it mostly explains everything, including that weird, little last gasp from Shepard at the end of the red ending, and why Star Child's voice becomes that of Harbinger when he says "So be it.". It makes those slow-motion dream sequences easier to stomach too, if you believe the indoctrination theory. As a fan of Freudian literary interpretation, it is also nice to think of Hackett as Shepard's Super Ego and The Illusive Man as his Ego. This would be more relevant if the indoctrination theory is to be believed.
Problem with the endings wasn't shit not making sense, or plot holes at all. Those are fine, so long as you execute it all very well. Case in point - Prometheus. That thing had far more potential plot-holes and unexplained logic, but most people who watched it don't really give a fuck or just rationalise it because it was still incredibly well done. People didn't hate ME3's ending because of plot holes, they hated the plot holes because they hated the ending.
You may well be right, that the community at large didn't hate the ending because of the plot holes. I, however, loathed the ending because it didn't make one jot of sense. I guess I wrote my last post from my own perspective on the ending.