Missiles advantage over a fighter is: No organics. This means that it can pull 60G thrusting or manevuers, while a fighter is limited to 8G and under. Are your fighters direct controlled (organic in the cockpit) or remote controlled? At remote controlled, they gain the advantage of having an organic computer (the brain!) in control of a fighting system not limited by organics (missile). After all, you can have a computer to auto-respond on developments that happen too fast for an organic, but the organic is there to handle things that the computer isn't an expert on (such as the current politically derived Rules of Engagement.

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I can see early space fighters having the pilot in the cockpit, and over time, moving them out and back to the carrier. That is what we are doing with modern fighters in the Real World. (See: Unmanned Air Vehicles (UAVs) and the Unmanned Combat Air Vehicles (UCAVs) for details). At that point, you end up with: Missiles. Multi-load, multi-function, reusable, but still, they are just missiles. A weapon carrying system that deploys more weapon systems. Or, put another way, a baby carrier.

I'm being extreme here, but the difference between a missile and a (sometimes) remotely piloted craft grows very blurry and indistinct when you get into missiles that deploy sub-munitions, and that are capable of taking their own evasive actions and determining their own targets. Indeed, most of the tech has been incorporated into the UCAVs, which are entirely programmable (like a missile) so that no input from any pilot is ever needed to perform their mission and deploy their munitions. Or shoot down other aircraft.
Now, reality doesn't matter. But I'm curious what having fighters gain us in terms of fun and strategy. Attack fighters will add to your ship's overall strength, but only be vulnerable to interceptors and point defense? Why not just make them their own category, and only allow intercepters to be be the defenders?
And shouldn't missiles be just as effective against fighters? After all, that's what we use to shoot down fighters now. Well, that, intercepters, and flak. I presume that Point Defense utilizes Flak (along with a mixture of short ranged, fast recharging, energy weapons and/or small mass drivers). Humm... come to think of it, the truth is that even energy weapons should be able to pick off fighters as easily as they can pick off any other space ship. Energy weapons require extremely precise targetting (otherwise, you miss. No self guiding weaponry there!). And your energy weapons have to deal with extremely fast moving objects (because you yourself are moving very quickly, and that will make even 'stationary' targets appear to move at those speeds). So why can't they pick on fighters? It's not like the fighter is only going to be 5 meters long by 1 meter across. You still have to pack all the weapons, engines, and whatever defense you want, even if you keep the pilot back on your carrier (thus letting you not worry about life support or life protection from high G maneuvers).
Again, I'm just trying to understand how it would all work together to add strategy to the game. And why fighters would be vulnerable to fighters (Space Superiority/Interceptors) and PD. If PD work just as effectively against fighters, then everyone would just use PD to defend against fighters and missiles, instead of picking something that only works against fighters, wouldn't they?
Humm... I recall Brad mentioning that ship defenses that your attack method isn't vulnerable to will still add between 1/10th to 1/2 their value to the defenders, with the final value to be determined in beta for best game play. Would fighters ignore that? Is that their special reason for including? Is that you can choose their attack method (ie, simple bombs (mass driver EQ) or energy bombs (Energy weapons) or missiles) before ever battle? That would make them an interesting strategic choice, but it would need to be limited so that it was only some fraction of what a dedicated system could. Then, we don't need a special defense against them, as your defender would defend against their defense method. After all, your ship's armor will just as easily absord and redirect a kinetic strike from an iron "bomb" as from a mass driver. And your energy fields will shift away energy from a local explosion as from a directed beam weapon. And your point defense will shoot down the missiles launched by the fighter just as if they were launched by a ship.
Would that be fun? A multi-purpose weapon system? It would provide players with similar strategic options that real carriers provide in the real world. More strategic choices means more fun, doesn't it?