Drew Karpyshyn never claimed to have come up with the concept of the Catalyst..... Vapor ware... Nor is it uncommon for games to feature data buried within itself alluding to unused, cut, or alternative stories/quests/plotlines, etc (even ME2 had a bunch of unused/alternative missions and story versions buried in its TLK files).
Just for the record... You're almost making the plot holes and the failures sound like an okay thing. I can see that you know it, it is a hard thing to go programing but cmon they're professionals. I didn't saw much of my past choices making that lot of difference as Casey Hudson promised for the ending, I barely saw some by the middle yes but not on the conclusion. The EMS and galactic readiness just looked important, and admit it, it was easy to achieve and it wasn't that important. We were being fooled and some people accepted it so easily, with no problems at all. ME2 had much more branches growing out from the gameplay for the ending, than ME3 ever had! He said it himself, he wouldn't deliver some A B or C kind of ending for us.... but aren't the Catalyst's choices exactly some A, B or C? After screwing it up they just came to the news saying what they wanted to do, but didn't? It is okay to keep on polishing the game until the game comes to the final state, but on ME's case it just compromised the whole game, They didn't even had time to remove the fossilized ideas from the files, this is a rare thing to find inside a game, this is evidence that Bioware had some heavy crapstorm happening inside their place. Me's problems made it look rushed and confused, and From the Ashes was just an insult. They would never guess we would find evidence inside the files.
My opinion here, the damn IT thing and the ending itself were just the nasty result of those things you said. It was confused back on 2012 because the game alone was just a big corpse of many dead ideas, scattered around some TLK graveyard. I will forever blame EA's "administrations" for that.
Edit = And I will also blame the devs for trusting their story's continuity for some fans to make it, instead of themselves. I will never agree with that "democracy" which plagues some writers freedom.