I'm glad nobody mentioned my little theory 
I've just spent thirty minutes arguing about this with PN. Personally, i think The Intruder is Commander Lock, bit out there but some things I noticed could point to him.
Now remember, this is just an speculation. I'm not actually SAYING it's Lock.
OK, first things first, the voice, sounds an awful lot like Locks to me if you try to listen past the "Transformers" voice.
Secondly, The Intruder, rumours that he is a free-born, like Lock.
Thirdly, Lock goes missing and The Intruder turns up.
Fourth, Not really a speculation about Lock, more of The Intruder. He asked "Where is the one i want?", if we assume that is Neo, then sooner or later he'll find the "shell" of him. Then perhaps he will go after someone that is closer to Neo. Perhaps Sarah Edmontons? I doubt that she would be mentioned and then just written off as a coincidence, perhaps the idea of her has been saved for now?
Fifth, my final and most bizarre theory but still sort of possible, "You are required." Perhaps Lock wen't insane with the power that he now perhaps has? Perhaps the Machines were planning to use him and he started attacking them because of his state of mind?
Anyway, that's just my theory, t'is also the end of my insane rant. Please for the love of god! Don't flame me for my theory, i'd appreicate replies but not flames.
Thank you.