A few possiblities:
1) Phasing missiles, that warp the Last few squares, thus skipping short-ranged point defense systems.
2) Armored missiles, like in MOO2, that can absorb high damage (PD weapons would have to become weaker for this to be realistic).
3) Energy/plasma torpedoes, that simply absorb PD fire without being affected at all. Or that get hotter and deadlier when exposed to PD fire
4) MIRV missiles - similar to the shotguns, the point is to overwhelm.
5) Cloaked missiles, that cannot be fired upon, or add +80% evade.
6) Laser-heads (like in Honor Harrington) that detonate far from the target (out of PD range), and use the detonation energy to pump a laser that strikes the target.
Of course, I don't know which of these can be added with the existing game engine, and having never played the extant mods, maybe some are already included.
-Cherry
7) PD's using supplies.
[ October 15, 2003, 22:02: Message edited by: Saber Cherry ]