The answer to your questions:
Common weapons: Skynet had not yet developed the plasma technology - there are prototype plasma weapons supposedly, but they are not yet in wide usage by Skynet's footsoldiers.
A common misconception is, also, that the machines are destroyed by the standard weapons. In the film there are actually no machines shown destroyed by conventional weapons - at least endoskeletons - but we do see one get destroyed by a minigun. The T-600 shot in the endoskull in the opening scenes of the Battle of the Skynet VLA is the same as the one that attacked John after the helicopter crash.
As was said though this is an alternate reality from the future depicted in the first film. Skynet progressed at a faster rate according to dialogue (which was oddly cut from the film) related to the T-800. Entire scenes were cut relating to John saying how Skynet wasn't supposed to have the Series 800 active yet during the briefing in the Resistance submarine. As for the components of the machines we don't actually know what the endoskeletons are made from yet. In TSCC, which has no relationship with the film series (well unless the new claims are true from McG), the 600 series is made of titanium while the Series 800 is a Coltan mixture.