»Trinity cannot be a program«

If Im right about the golden code in the real life, that Agent Smith could be seen because of the fact that he was a program. Then Trinity cannot be a program becuase... There wasn't any golden code on her.

Ooohh, another thing I was wondering. When Neo kissed Trin, how would he know where her lips were

I was thinking the same thing (how he knew where her lips were). I think it would have been a nice touch for him to have "missed," at least the first time. Had they done this (and shortened the scene by 20 seconds or so) it would have brought out a powerful comparison/juxtaposition: He is more machine than human at this point yet he demonstrates the most human attribute, intense love.

Have you ever kissed the person you love? You don't need eyes...It doesn't take "The One" to figure that out.

The whole searching around and not seeing Trin at first was just a device for the audience. So we could be shocked that she was a pin cushion.