OK, the internet needs another of these threads about as badly as it needs another cat video...
Read a comment from Bipolar Potter in the house rule thread about not letting an opponent roll green dice against ordnance just like a proximity mine. That seems a little too strong to me as some of the torpedoes become insta-kills for interceptors etc.
My $0.02:
Errata: When defending against a missile/torpedo secondary weapon, the defender's agility is decreased by one.
Would that be enough to make you carry ordnance? Has somebody proposed this idea already? Seems like it would help cluster and homing missiles more than the rest but wouldn't be too crazy.