Its ok the Extended Cut saved it.
It really didn't. It addressed none of the deep problems with the ending, only glossed over a new coat of paint on a sinking ship. There were serious problems with basic plausibility, a genre violation, and overall a very poor ending concept. It put the player who was paying attention into an impossible position; there was every warning sign imaginable that Shepard would be very unwise indeed to trust anything the apparition in front of him said, or suggested, but the game didn't even allow the player to express scepticism, in the dialogue, about what he was seeing being real, OR the apparition being honest.
The extended cut didn't add any such dialogue options either - and I know exactly why. Because if such obvious, and very called for scepticism WAS expressed by Shepard, there's nothing at all the apparition could say to mitigate those doubts, as the very form he took proved he was already in Shepard's head. After such scepticism, the "reject" option would have been the only reasonable path, but then the game would have ended up punishing the player for taking the only reasonable option.
The only thing that would have saved the ending would have been a complete re-write, scrapping at least everything after the last scene with Anderson, and creating a new ending, with a different concept. Alas, that was not to be. 