And here lies the problem.
By retconning or declaring one ending non-canonical you are basically devaluating someone's entire experience. This would provoke an even greater [censored]storm then if they tried to neutralize the entire situation somewhat, so the story fits for both endings.
I mean I fully understand that you want your decision to have an heavy impact on the storyline, but I hope you can also see my point that I wouldn't want my characters story to be declared completely invalid.
Just look at Mass Effect. In the last book sorta implied that Anderson was not a council member, which overall isn't even a major plot point, but still managed to cause a riot.
You have your preferences, and I have mine. And mine are that I don't care if my "experience" is completely "invalidated." What I
do care about, though, is the strength of the story, which can only be built upon strong foundation of backstory. If said foundation is just this flimsy mass of interchangeable parts forcefully shoehorned in, then the integrity of the whole plot is compromised. Udina being the human Councilor certainly would not be a choice I'd seriously make in
Mass Effect, but if the author of the novels thought it would suit the purpose of his story better, then more power to him, I say.
Truth be told, when I play an RPG, I don't see myself as an active agent in how the story
should unfold; I see it as a way it
can unfold, namely if I was the one at the helm. Events A, B, C, and D may have been what happened, but I get to see what happens if events W, X, Y, Z occur, if I so choose. This whole save transfer nonsense Bioware has gotten so obsessed with isn't doing it for me. In ME1, it allows me to make a decision on the structure of the single most powerful governing body in the galaxy. Naturally, one would expect this to have quite an effect on the plot in the sequel. It doesn't. What you see of Council space in ME2 is the same regardless of what you pick, the Citadel still has ridiculous (and completely worthless) security measures put into place, there's still some crooked politician running for office in Zakera Ward with extremely strong anti-human sentiments, and the Council, regardless of whether it's still alien or completely human, still won't give you the time of day. Really, the biggest consequence of that fateful and climatic decision you make at the end of ME is whether or not you get to see a Turian make quotation marks with his fingers.
Overall, in the wake of the save transfer between ME1 and ME2, the whole
world universe of ME just feels kind of generic, like there's no real sense of causality. And my decisions, despite the way they're presented when offered, are merely being acknowledged without really having much of an effect at all.