Questions
Spoilers:
The Skynet facility is a complete Terminator factory, full of active Terminators and surely many more ready for deployment. If the machines had to think "radically," why did they not send more than one Terminator to kill John Connor as soon as they detected his presence in the facility?
In a related note, the facility is full of nuclear fuel cells. If John Connor is so important to the machines, why not just obliterate the place, killing him in the process?
Similarly, why were the machines incapable of taking control of Marcus, for example, to prevent him from saving Connor at the lake? Or to kill him himself? Or to prevent Marcus from removing the comms/control chips in his neck? Or to prevent him from waking up at all? Or at least delay his reactivation until after the death of Connor, so to keep Marcus out of the equation?
Why is Marcus an advanced prototype, the only one of its kind? Skynet seems to have the industrial process of grafting human living tissue over a machine pretty much down at this point, even being able to fully repair Marcus in a matter of minutes. The machines could have sent more than one infiltration unit to get the job done.