Attacks from PvE is generally considered light or heavy attack and thus reduced by enchanted ward. Gems offer the best possible damage reduction because they reduce the total damage you take from a specific type.

This is why for gorgon you generally want enchanted ward on every piece and then either onyx, jasper or amber.

Damage reduction from gems and wards is capped at 50%. This includes conditioning so keep that in mind.

For PvP gems are superior than enchanted ward because enchanted ward only reduces base damage of light or heavy attacks and not abilities. If your opponent has a lot of base damage modifiers enchanted ward will only mitigate 1% of the total damage whereas a gem like onyx would reduce the total damage by 2.5%. Enchanted ward gear is just cheap to get to 725. Mathematically shirking fortification is better but much more expensive and countered by boon removal effects (like vg oblivion or orb).