I'm probably going to regret this, but what the hell, I'm game for some discourse.
First of all, Those-That-Came-Before aren't explicitly called aliens, they just came before man did. One could assume they're aliens, but aside from a Piece of Eden showing up on the moon and their advanced technology that's all you've really got, which just proves they've seemingly been to the moon (so have we, we aren't aliens). It could be they were the first civilization, a form of man that developped before homo sapiens, and then they made homo sapiens what they are today. So its a bit of a twist on the old cliche. Speaking of the cliche, just because its been done doesn't make it a bad thing. Ask yourself if the cliche was done well and if you didn't see it coming. The latter usually adds emphasis to the former, but they don't preclude each other.
I also disagree that it made the entire plot of the game pointless. Ezio's storyline more or less wrapped up when he decided to not kill Rodrigo, just deny him his prize and leave him broken. The contents of the vault were there solely for the series' B-plot, which is an important framing device: it shows how the past can directly shape the future, and pulls one hell of a mind-game on you when Minerva breaks the 4th wall.
Quite frankly using the word travesty feels like serious hyperbole here. I mean, I can respect people not liking it, as Desmond really is uninteresting (I don't using the word bland though even though it should work), but I can't see what else the vault could of contained that would of made it better. The game instead gives a good sequel hook after the big bad's been beaten, though granted the hook isn't the greatest since its another list of things that people need to find like in the first, only this time its temples instead of Pieces of Eden. It works though as, like the first game, it implies the present day will be vital but the Animus could be used yet again to find the other temples if someone in the past found one.
I will comment that I like how they explain the concept of demi-gods and such, with the first assassins being as such. It explains where the Eagle Sight comes from if nothing else. The parkour and such, those are pretty much training, though they could probably mention that they're naturals since so many of their ancestors have done it. I mean, Desmond and Ezio were both lousy fighters when they started out, but thanks to training they're awesome and they both picked things up reasonably quickly, granted Desmond cheated.
So yeah, I didn't mind the twist, I think its one of the most well-done storylines in gaming since it ties together the world's rich history in a very elaborate way that makes a weird sense.