A bit thick on the hyperbole, but essentially yes. THe entire middle portion of the trilogy spins its wheels regarding the Reaper threat. THere are plot points that go nowhere (Hades' Dogs in ME1, Haestrum in ME2). THere are important choices that are trivialized or go nowhere (Human Councilor chocie, Collector Base) THis story didn't "evolve" it was practically stream-of-consciousness.
So if the second Mass Effect feels disonnected to the reapers threat it means that they don't know how to end? That's nonsense. You're ignoring what have been set in Mass Effect 1. For Haestrum in Mass Effect 2, it goes nowhere? I usually prefer to use video from the game but it would be too long so here :
http://masseffect.wi...iki/Dark_energy
and in this one "Javelin missile launchers" and "Conrad" :
http://masseffect.wi...Assets/Crucible
It doesn't go nowhere, it goes where you didn't want it to go because you were expecting a dark energy ending (which is a total nonsense if you only played the game and didn't take care of the internet speculations).
And for the choices you have to blame Mass Effect 2, not Mass Effect 3.
And anyway, ignoring that something like Mass Effect is such a huge work that the ending couldn't be entirely written since the first Mass Effect, this just shows that you don't know what writing is.
General Oraka tells Shepard he/she would make a good general someday. Is that a "clue" also?
No. You totally misunderstand it. I won't give you answers, you'll have to understand with the clues given by the game itself.
It's a pretty common phrase in the trilogy. If you pay attention

So you can't see the difference between the narration and how the character try to act. You're trapped in your own representation of the game, you didn't really played the game, you played what you wanted to see, ignoring the writing of the game.
Basically, I wanted to see how it ended for my Shepard. I went into ME3 with very low expectations, and it couldn't even meet those.
With low expectations we don't spend years saying that it's bad writing... 
Illogical, disjointed narrative, ooc behavior in characters, "ass pulls".
The problem is that the ending is not like that : not illogical, not disjointed etc...
Just because someone is trying to weave a complex story, doesn't mean they succeed. I can try to prepare a big fancy banquet. Doesn't mean I'll succeed.
I agree and the Wachowski are an example. They do "complex" stories but in my opinion, they don't succeed. But they try so I don't criticize that point. And I'm glad they try.
Actually I used it as a reference because it was also the end of an ambitious science fiction trilogy that turned out to be hugely disappointing. That Mac Walters invoked it is simply a piece of delicious irony.
Don't tell me you don't know that. You quote Mac Walters with "lots of speculation" and on the same document you've got that reference. It has been said again and again on this forum. You know that it's a reference. But actually I'm not sure that it's Matrix 3 ending, I think it's more the architect discussion the reference. That's why I don't think you're honest when you're saying that.
Well we agree that the ending is the most important part, at least. But I still hold that Bioware disagreed. Because it doesn't make sense. Not unless you play specific Shepards and make particular choices.
It makes sense. If you don't understand, you should read Nietzsche. "Doesn't make sense", "pseudo intellectual" etc... all of these are just what people say because they don't want to think. It's easier to say that.
PS : "A strong argument for that can be made too. And part of the reason I dislike ME2'S opening." You dislike one of the few story part of Mass Effect 2, a very important part of the trilogy. Then why did you play Mass Effect 3, even with low expectations, if the story is not what you were expecting? Low expectations but 3 years hating the game while you admit that the story isn't what you like. That's strange, isn't it?