well i think he is the one but not just another one, he is something much bigger. plus when you have someone like Neo you need an anti-neo who is just as powerful or more so. Smith will fill in that role and i dont know how but he will be just as powerful as neo by time their final conflict takes place which will decide everything.
Neo is not part machine...here is the thing...Neo is just another one ladies and gentlmen, sorry to break it to ya...but He is special in the regard that when faced with the decision of the two doors...he chose the one to trinity...Maybe being in the matrix and in the real world longer then the former ones has made him realize something...Here is the reason for the machine control thingy....Neo can pretty much control things in the matrix...well the matrix is just a big machine...like the machines in the real world, it's the same damned technology created by the same source...so he realizes this and then he can stop any machine connected to the machine mainframe/source it's really simple once you think about it...as for Smith, (I've seen revo) When they face off, neo and smith...smith is stronger...