-Why did Skynet not know the location of John Conner's (HUGE) resistance headquarters? ESPECIALLY after it is established that any "abnormal" sounds, like a radio playing, let alone huge fucking explosions all over the place, will bring out Skynet drones/Terminators to the area, (and nevermind the radio signal that they discovered that de-activates robots is actually being used by Skynet to track humans!) The resistance blows the shit out of their own mine field and wastes tons of ammo trying kill one of their own people and Marcus, and nothing happens.

-In the same scene, right after the mind field part, John Conner is in a chopper with some other guys investigating a nearby river. There's little Skynet fish-like robots in there that kill everyone but Conner. Again, this is right near the resistance base, so why doesn't Skynet know where they are?
-The "comic book villain" like portrayal of Skynet and its speech to Marcus, revealing all its plans. So fucking cliche. It used Marcus to lure John Conner and Kyle Reese to it. WHY? It's supposed to be a cold, calculating machine. It had multiple chances to kill Kyle Reese in particular outright, but did NOT.
-How is that Marcus Wright's cybernetic parts are so much more advanced than the Terminators that were created
after him? Not to mention, if he was so successful for Skynet, why bother with T-800s at all? Why not make more human/terminator hybrids, since it's much harder to tell if they're "robots" or not?
-How easy it was for John Conner to take out the various Skynet drones alone, and for him to sneak into Skynet by himself with no problems whatsoever.