Alzrius
The EN World kitten
For those interested, I wrote a short sidebar that deals with the questions of how this question (high-tech weapons and armor vs. magical weapons and armor) could be easily resolved in a d20 system game.
Looking over the new armors listed here, you may realize that, in terms of statistics, armors from one Progress Level are relatively the same as another. A Vanadium Covering, for example, doesn’t seem that much different than a Neutronite Aegis. However, given that the latter armor was developed in the future from the former, shouldn’t it clearly offer better protection?
In regards to weaponry from previous eras, it does. When weapons from a lower PL than a suit of armor are used against it, the wearer gains DR X/--, where X is the different in their Progress Levels. For example, while wearing a Nanofluidic Suit (PL 8), you would have DR 2/-- against damage from a Laser Pistol (a PL 6 weapon). When a weapon from a certain PL is used against armor from a lower PL, the weapon gains a circumstance bonus to the attack roll equal to the difference between their Progress Levels. For example, someone using a Laser Pistol against a target wearing a Duraplastic Breastplate (PL 5), would have a +1 circumstance bonus to their attack roll.
If you’re using FX in your game, then consider altering the above rules slightly. Magic (or psionics) transcend the limits of the physical universe, and make it possible for even a primitive weapon to penetrate a powerful armor (or for a weak armor to resist a futuristic weapon). When using FX, armors of a higher PL than an attacking weapon gain DR X/magic. Likewise, weapons of a higher PL than the armor they’re attacking do not gain the circumstance bonus to the attack roll if the armor has an enhancement bonus. Fantasy d20 weapons and armor are all Progress Level 2. Natural weapons and unarmed strikes are PL 0.