The problem that you run into is John 1 - in which it says of Jesus, that by him all things were made, and there is nothing that was made that He didn't make. This is why the Nicene Creed is so careful to say he was begotten not made. If God the Father made Jesus, then John made a boo-boo.
The incarnation, on the other hand, is merely putting flesh to that which already existed, namely the spirit of Christ in the man Jesus. The physical manifestation is well known to anyone who has watched a science film on conception.
In other words, the spirit is eternal, but the flesh is temporary, and created.
The fun part, however, is that since it is something made, it means that God the Son got to make his own body. (Reminds me of an episode of ST:TNG called The Offspring, in which Lt. Cmdr. Data's daughter gets to choose her form) I find it interesting that He chose to be so normal and plain- but that's who our God is- he wants so desperately to be with us, that he chooses to be just like us.
The debated part of the incarnation is the nature of the Spirit/Soul/whatever of that flesh in relationship to the pre-existant Spirit of God the Son. The relationship of that spirit of God to the flesh of that baby born is the root of most Christological heresies like Nestorianism, Apollinarianism, and Monophysitism. Here's the "problem" of each:
Apollinarism: Says that the flesh that was created had no mind of its own. The problem with this idea is that God was never actually a man. In its most extreme form docetism Jesus only appeared to be human, and was in fact, merely a 'phantasm' of the flesh - a solid spirit that had no human substance whatsoever. That basically denies the incarnation altogether.
Nestorianism: Says that the flesh was just a normal guy whom God the Son indwelt. In this idea, Jesus was schizophrenic, having two distinct personalities in one body.
Monophysitism: Says that there was only one nature, in that the human nature was so dissolved in the divine that it basically ceased to exist. Of the "heresies" listed, this is probably the closest to Orthodoxy, but fails insofar as it denies the existence of a human will.
The orthodox position is the so called hypostatic union. It says that Jesus was fully God and fully man. (Hey, Jesus is just 200% that's all!) It's a bit tricky, but the basic idea is to ensure that any Christology recognizes that Jesus was fully able to fully be both things to fully accomplish what he was sent to do.