[Shotokanguy]

Coming up with an explanation that makes sense in the PS universe is the best way to go, IMO.

Say something like...

Vanu weapons use different kinds of energy against different targets, so an AV weapon doesn't do as much damage against infantry.

The TR flak could hit with plenty of force, but just say that the shields the soldiers in PS2 are using are highly resistant to kinetic energy.

And if the Gauss rifle is based around kinetic energy, say the magnetic systems for the bullet cause interference with shielding and allow more penetration.

Just silly stuff I made up off the top of my head, but the point is I do want each type to be less effective against the other two. The best way to do it is to think of some reason why it shouldn't do it, and have that take effect in gameplay. So maybe the flak from the Burster won't get through shields for a while, but if you do, you can take down infantry quickly because health has no natural damage resistance.