[Suicide Junkie]

Seekers work just fine targetting fighters.
Seekers work just fine targetting other missiles, too. (Needs v1.94+ in simultaneous mode)

Never EVER make them point defense, however. In such a case, every single PD missile in your fleet will be launched at the first fighter/seeker to move. Really bad tactics.

Instead, let your ships all fire on random targets manually. Instead of 150 missiles pasting a single stack of 5 fighters, you can have a beautiful wall of seekers popping fighters throughout the enemy fleet in a massive bombardment.

Note: this also presumes that you do something to fix PDCs, so that missiles are worth using, yet at the same time not overly powerful.
Turning off the auto-fire is one of the best things you can do.