The WC3 shields ARE the same shields that were used in WC2--it's just that over the intervening couple of years both the Kilrathi and Confed have brought in a new generation of fighter guns that can penetrate them. Then in Prophecy we see a new generation of shields.
Basically, locking guns or torpedoes (or missiles) onto a phase-shield-protected target is a cryptography battle. It is a race between the attacking ship's computers trying to decipher the defender's shield patterns, and the defender's computers trying to change the shield patterns unpredictably faster than the attacker can keep up.
This means that when only capships can carry powerful enough computers to defeat the defender's computer, then only they can pierce shields. Once they become available in bomber-sized craft, then torpedo bombers can be used. Finally, when a fighter's computers can figure out the shield pattern in the interval between gun shots, it becomes possible for fighter guns to pierce the phase shields. When that happens, there is a sudden incentive to invest in even MORE powerful computers (and faster-responding shield generators) for the capships so that they can become invulnerable to fighters again, and the cycle repeats.