I realize that this game is still in development, and that Alex probably gets all sorts of suggestions along the lines of 'add my awesome weapon/ship/module idea', but I think I do have a suggestion that could possibly increase the complexity of gameplay with new mechanics.
Anyway, here we go: missiles and torpedoes are all pretty basic. I was happy to see the Salamander MRMs get added in, because of how they work, but for the most part, missiles do varying amounts of damage, move at varying speeds, and track targets with varying competence, whereupon they slam into them and deal damage. Pretty basic.
But the beauty of guided munitions-- indeed, of any substance weapon (as opposed to an energy one)-- is load variability, tactical flexibility. So I have a few suggestions to lend that sense to guided munitions in Starfarer; they can be taken on a case by case basis, all, or none, hell, I'm just talking.
1) Improved Torpedo/Missile Magazines: In Starfarer, you can already scroll through various weapons in a weapon group if they're marked as 'alternating'. In 0.35a, I found myself doing this pretty often on the Apogee to avoid wasting Hurricane MIRV when all I wanted was Pilum LRMS. I think it would be useful to handling different varieties of warhead if you could scroll through different loads to select what you'd like to use. It'd still count as one weapon on the refit screen, but you could choose to carry magazines of, say, HE warheads, and maybe a few HEAT rounds for those tricky Dominators. This could apply to cannons as well, but that might be a bit of a hassle.
2) 'Nova' Missiles: Optics and electronics are delicate things, and designed to operate within a particular band of stimuli. 'Nova' Missiles are essentially space flashbangs, low yield nuclear weapons that give off a lot of flash and radiation, but don't actually do much damage-- and are in fact designed to detonate away from their targets to maximize coverage-- but which confer a penalty to turret accuracy to ships caught in their radius for a certain amount of time dependent upon the quality of the crew. It works through shields, after all, ships need to be able to see through their own shields, so it's a useful thing for close assault ships to have as they burn in to bring their close range weapons to bear. Alternatively, could be used at a distance to support wings of fighters coming in on a particularly hard to approach target.
3) Minelaying Missiles: What it says on the tin. Being that they are more strategic, rather than tactical, weapons, minelaying missiles would be launched from the tactical map, and designed to disperse bomblets within a certain area. More or less useless against anything heavier than a frigate, but useful for inflicting attrition upon incoming fighter wings.
4) Interceptor Missiles: Small, but plentiful, these missiles are useful for bringing down fighters and torpedoes. Lacks the longevity of other point defense systems, but packs enough of a punch to down heavily armored torpedoes at a generous distance.
5) Beam missiles: In real life, there are serious drawbacks to the usage of energy weapons in space. For example, a bomb-pumped x-ray laser requires, well, the detonation of a bomb to power its discharge, creating not-easily-dissipated heat and increasing wear and tear on internal parts. Beam missiles solve this by taking those pesky issues and moving them outside the ship. Basically, beam missiles fly within a certain radius of their target, and then explode, pumping an onboard laser array and firing a beam at their target. The advantage of this is that it'd do energy damage, as opposed to frag, high explosive, or kinetic damage, and that a beam missile would strike its target from outside most point defense ranges. For the sake of balance, this would mean that beam missiles would probably be less potent than conventional loads, but you could still harry an enemy enough that they'd be forced to close on you just to shut you up, allowing your fleet to hammer them as they maneuver.
6) Probes: Pretty simple. Instead of scouting with a wing of fighters with valuable stuff like weapons, armor, and people strapped to them, why not shoot a missile instead? Probably needs to be either dumbfire or fired from the tactics screen.
7) Point Defense Spoofing Missiles: Another idea ripped from real life. Modern antiship missiles fishtail wildly when they get close enough to their target to shake off CIWS fire. More effective against ballistic point defense, but packs a smaller warhead because of all the equipment needed to make it move so erratically and still land on target.
8 ) Decoy Torpedoes: Torpedoes that throw out warship level heat, radio, and radar, designed to throw off missiles at the last minute. Pretty high velocity, and in limited quantity. Small operational radius, and doesn't necessarily work on all incoming munitions.