So many plot holes, i wish i can ignore Spoiler

Rating: 4/10 (30 May 2009)

I love the Terminator franchise, but T4 could be so much better if the plot holes was explain .
Spoilers
* * * John Connor was still only a mid level commander , the high command won't even pick up his phone call.Why would Skynet use so much resource set up a trap to catch him and Kyle?
And how did Skynet know about Kyle 's connection to John?
Kyle was just a teenager , a nobody civilian ,And recognised Kyle's face in a computer scan ?
John just trust Mucus just after he save John's life.But they just make up a plan to rescue Kyle within a minute and exchange a few word and hand him a communicator device.
If the Resistance can have large base and airfield, why did skynet just nuke their base or spread bio weapon into human area.
And skynet repair Macus 's organic body , and no guards ,no T-600 watching over him , he can just smash his way out of the lab.
Would Guerrilla Warfare tactics make more sense than sending a large fleet of choppers . The Tech-com high command sub boardcast underwater the shut down signal,and let skynet aircraft attact them from the air. They could just board cast the signal in with large sateille dish like the one in the beginning of the movie , and when the sub detecting hunter killer, they could just shut down the boardcast and dive deeper and escape.
Where is the resistance get spare parts and fuel for their aircrafts. They lost a lot of chopper and A-10.
The motorcyle robots, Skynet make their shape so easy for human to sit on them.So John just catch one and override the computer, and he got himself a fast moterbike.
Does the T-800 with Arold's CGI face have to be naked waiting for John?
How did Mucus knew his heat and blood type are suitable for John?