The more I think about it, the more I love the ending.
The books wouldn't stay with you half as much if the ending was just a run of the mill 'happily ever after' ending. I guess it's one of the things that makes the third book so emotionally powerful. And I think PP wrote Lyra's desperation in that scene (where Xaphania tells them they must seperate) so strongly that it really gets at you.
I agree, I only said my theory for the sake of argument, it would completely ruin it if the ending WAS happy, (and I think that my theory would work, because Sir Charles Latrom managed it, why not Lyra and Will?) Pullman IS a great author or else this whole forum wouldnt be here right?