THERE BE SPOILERS BELOW:
I didn't actually mind the lax security at Skynet because they were prepared for a global offensive (and so would be scattered thin) and believed they had adequate surveillance in place of all major forces. Granted, I thought it was faulty that the machines couldn't seem to figure out or detect explosives (let alone disarm them)...
Also, why naked & unarmed? They weren't traveling their time. And why keep Reese alive at all (even if they didn't know he was JC's father)?
That was the only parts that jumped out at me. Ok, even with their forces scattered thin, I'd think that some "Resident Evil" type traps could be in place as well, or even entire areas with toxic gases (to humans, not machines) being a common security feature "just in case." But maybe Skynet, made in its creator's image, was just as full of hubris as the ones that created it? :p
What I think would be interesting is having more than one infiltration unit and showing how different humans adapt to their conditioning. Ironically, a good soldier that follows orders without question would've been far more ideal and far more likely to go with Skynet's plan than a death row cop killer. Stupid Skynet, just doesn't understand humans.