I think C&C was always about art and not a StarWars like canon.
You can compare lots of things from C&C with reality.
Tiberium was loved for being such a good energy resource. It's spread was accelerated so energy concerns could achieve higher income. But being blinded by the money the chain reaction has started. The spread of Tiberium was going out of control. Tiberium started to appear where you thought it wouldn't appear. The world is getting polluted by Tiberium. You can compare the whole story of Tiberium with the global warming triggered through the industrial revolution.
Nod represents the worst things religion has ever brought up. Such as total fanatism and crusades like wars. Also it is an icon of terrorism. It is even mentioned in Tiberian Dawn by naming several terrorist organization which are linked to Nod.
GDI represents the western civilization or maybe the USA making wars for their interests like supporting the civil war in Africa (TD).
The Tiberium Wars:
- The First Tiberium War was a war for Tiberium
- The Second Tiberium War was a war against Tiberium
- The Third Tiberium War is a war to survive Tiberium
It also seems like GDI is becoming dependend on Tiberium by learning how to use it. We don't know much about the third faction yet, but I guess they could represent what happens if you come dependend on Tiberium. There are some things which hint this:
- The Aliens get more money for harvesting tiberium, so it seem like there is a big request for Tiberium
- Several weapons of them are based on Tiberium or use Tiberium to power themselves up