[Heatmiser]

It is obvious that there is something different about this Neo than the others- that being his love for Trinity. The architect tells him that he gets to some conclusion more quickly than his predecessors and the Merovingian is surprised by Neo's abilities, especially since he says "I have survived your predecessors and I will survive you too."
I think it goes back to Neo's 'joining' with Smith in Matrix. That was something that none of the other Neo's had ever done before. It changed both of them. The way that Smith can clone himself on a human being inside the Matrix and then 'possess' that person, or plant suggestions in them to carry out actions outside the Matrix- the guy who tries to knife Neo, but stops when that kid comes up behind him. And the other side is Neo's ability to sense (and maybe stop) the Sentinels- there is debate on whether he stopped them or not. Why wouldn't the architect lie? I think as a machine, he wouldn't be bothered with anything resembling morality, but the most pragmatic solution- the best for him and maybe the machines as a whole- would be his motivation and whatever he needed to do to accomplish that is what he would do. So either he lies when he says that if Neo chooses to go back into the Matrix- he says that Trinity is going to die and there is nothing Neo can do about it- so either he lies to get Neo to do something he wants him to do, or he underestimates Neo's abilities and/or his love for her- he doesn't know that Neo could actually bring her back to life.
Hmmm.... still thinking ... It did help to watch Reloaded a second time at least.