Good point, freak.
And welcome to the board! :wave:
Smith did say that something happened... something he doesn't understand. He seemed pretty mad that Neo got up in that hallway: "I watched you die." But Neo's resurrection triggered a very illogical response in Smith: he attacked Neo with hatred. I think this is when he realized that Neo had a purpose.
However Smith was resurrected (even he doesn't know) he came to feel more, become more emotional. Maybe this is how he came to realize that some part of Neo might have been merged with him. There's some element of humanity in Smith now. He has desire, drive, ambition, or, in his words, purpose.
He goes into a speach about purpose just before he tries to overwrite (or remake) Neo, when other incarnations of him show up. Purpose drives him and defines him. That's what he decides to take from Neo: his purpose.
Maybe he couldn't because Neo isn't completely sure what his purpose is: he still doesn't know WHY he's the One.
Hey, here's something else I remembered. During the Key Maker's story about the building that houses the "source", Neo has another vision, one in which the building itself seems to be infected, growing blemishes or tumors that knit together, then explode. The fact that these blemishes are the color of fire, and that Neo explodes out of the building in a blaze, is it simply a vision of what his action would do to the Matrix?