It was hybrid Tech and much like the T-1000's, still really hard to create and its obvious that Marcus was specifically picked for this role for some reason, so there might be reasons he was the only one. The fact that the HK readout listed him as Marcus wright and not a unit model points to this being the truth.
The Bases, yeah that was kinda of really retarded considering the fact that the other movies, books, the TV series, etc state that the bases are all underground and well hidden. But remember that Kyle also stated in T1 that you could only move at night, while the opposite was stated here.
The radio thing is also really lame I'll admit, skynet is in charge of all military tech and satellites, so picking up on a transmission should be easy. Maybe Skynet isn't as advanced as we are lead to believe.
The T-600 wore clothing in an attempt to try to lure humans to them, remember that from a distance Marcus thought the T-600 was human.