You don't really have to maneuver if your weapon has range. And any weapon you want to put on a fighter, I can make more powerful/better range and put on a ship. And protect that weapon with heavier armour/shields.
But how well can you aim it? It doesn't matter if your death ray can fire 1,000,000 times further than my death ray can if my death ray can be mounted on something that your death ray cannot reliably hit from beyond the range of my death ray, and it is not necessarily true that adding armor will necessarily improve the survivability of vessels; certainly the current trend in naval design seems to indicate that passive defenses (namely armor) are an insufficient answer to the threat posed by modern weapons, to the point that modern warships are effectively unarmored even at the capital level.
It also doesn't matter if your death ray is 1,000,000 times more powerful than mine is if both of them are capable of killing the same kinds of targets; yours just hits the ridiculous overkill level far faster and could therefore be less efficient. And in GCII, the indications are that weapons are at a point where capital-grade weapons can be carried by fighter-size vessels; since GCII doesn't include more powerful weapons for capital ships, that would tend to indicate that either the weapons in existence are at the upper limit of what the factions can currently produce, or that there is no particular need to build even more potent weaponry. Granted, this is an aspect of GCII that I would be happy to see change, but it is what it is.
And of course, your fighter is still travelling slower then my ships, since the ships can have bigger engines. Unless there is some upper bound that everyone hits for speed. So any direct LOS weapon will never get to fire, since the frogman swimming with his harpoon will never reach my sub.
Bigger = faster is not necessarily true. Larger vessels will require more and/or more powerful thrusters in order to attain the same accelerations as smaller vessels, and additionally the structure of a larger vessel will be more severely stressed by said accelerations than the smaller vessels will, and will be particularly vulnerable to bending moments when the vessel rotates. As a result, there are real-world physics reasons why larger vessels might be limited to lower 'speeds' in combat.
Additionally, if we assume that combat takes place at sublight speeds (which I would think reasonable when the available categories of weapons are 'mass drivers', 'beams', and 'missiles', especially when the basic 'beam' weapon is the laser, which cannot possibly describe a weapon which propagates at superluminal velocities if we assume that the weapon names used are even remotely accurate descriptors), then we have an upper bound on the speed of the vessels involved - c - and most likely the in-combat speeds are substantially lower since the missiles and projectiles take appreciably more time to reach the target than the beams do and yet the vessels involved cannot outrun them, and at least one of the beam weapons should propagate at the speed of light. We can also infer from the fact that one of the weapons is a laser that the upper bound on the engagement range is likely not more than a few light-seconds, although this is a much more questionable assumption than that the speed of the vessels during combat is not greater than the speed of light.
It is moreover a false assumption that a line-of-sight weapon will never get to fire due to an inability to reach the target, as that would indicate that in the setting missiles are far and away superior to beams and mass drivers, yet the performance of all three weapon categories is comparable. Therefore, line-of-sight weaponry must be able to reach a suitable firing range despite the theoretically superior engagement range of guided weaponry.
Lasers and power transfer beams work on exactly the same principles in many cases, so they're not less efficient so long as the fighter does something useful that a laser cannot.
I would tend to think that the point is more that if you can hit a fighter with a 'power transfer beam', then you can most likely hit a larger vessel with the same beam. And without significant energy storage on the fighter, the 'power transfer beam' would need to carry a power similar in magnitude to any beam weapon that the fighter might carry in order to allow the fighter adequate performance (using beam in the sense of the GCII weapon category). Of course, since the fighter's weapon should be much closer to the target than the origin of the 'power transfer beam', the fighter's weapon could be better-focused and perhaps better-aimed, though this does not address the issue of fighter survivability in the combat environment.
Additionally, 'power transfer beams' do have a potential loss of efficiency relative to a weaponized laser - namely, some portion of the power carried by the 'power transfer beam' is almost certainly being used to power some portion of the fighter's systems, which represents a loss in energy delivered to the target even if there are no energy losses involved in the internal mechanisms of the power receiving system and the weapon system used to translate the 'power transfer beam' into attacks on the target vessel. Obviously, internal efficiency and intensity loss through beam spreading are going to determine at what point it becomes 'better' to use the fighter than to use a more direct method of attack, but you cannot claim that a fighter need not carry its own internal power supply and then argue that said fighter can translate 100% of the power of a proposed 'energy transfer beam' into an attack against a target.
Galactic Civilizations has anti-gravity and inertial compensation.
Which is not necessarily a guarantee that manned craft can sustain the same kinds of accelerations as unmanned craft, as that assumption would require that inertial compensation and/or artificial gravity be capable of protecting living beings from accelerations up to the limits imposed by the vessel's structural strength or engine and thruster capacity. All real systems have limits; it isn't that much of a stretch to assume that even magitech in soft sci-fi universes likewise have an upper limit to their performance.
Bigger ships are harder to accelerate and maneuver due to their massive...mass. Missiles are guided by unintelligent computers. Only fighters, preferably piloted by sapient machines, would have the ability to out maneuver the enemy and bring firepower to bear on specific targets in a dynamic, 3 dimensional battlefield.
But do they bring enough to the playing field to justify the cost? If I can use a 1 million dollar missile to shoot down a 1 billion dollar fighter, was the fighter worth bringing to the party to begin with? Am I better off swamping the enemy defenses with million dollar missiles (of which I can afford to lose 1000 times as many as I can afford to lose of the billion dollar fighters), or am I better off with the presumably more accurate fighters?
Based on the fact that in GCII there exists a hull category similar to modern-day fighters (the Tiny hull category) and based on the fact that these can be made to work reasonably well at certain points in the game, or under special conditions, I would say the answer to the above questions are more in the line of 'maybe' than either 'yes' or 'no', though tending more towards 'yes' than 'no'. If we want to look at it from a realism perspective, which is at best marginally helpful since Galactic Civilizations is much more of a soft science fiction setting than a hard one, then the answer is still very much a 'maybe', since we'd need to know something about targeting performance, guidance accuracy, countermeasures, and vessel performance in the Galactic Civilizations setting before we can come up with a reasonable answer based on real-world math and physics. And if we want to look at it from the so-called 'developer's intent' point of view, then the answer has fairly strongly been indicated to be 'yes', although I don't know that that is certain because I don't recall them saying anything specifically about starfighters, only about carriers - though I could be wrong as I have not watched either of the podcasts, so if there were something there I would not know of it.