"and to navigate through hostile space they'd be the slowest."
WRONG. Large ships have larger engines and more fuel, and probably larger and more powerful Bussard ramscoops if you consider that piece of tech to be present. They can attain higher top speeds and go further, even though smaller ships might be able to accelerate and turn faster thanks to their lower mass.
"Good luck docking with an enemy ship while it's still shooting at you."
Good grief. After ramming, this is the second dumbest combat tactic I've heard of. Why the HELL would the enemy let you dock with them and have a close-quarters boarding fight? I'd just blast the troops to dust in space itself. Whether they're coming at me on a capital ship or on a flying carpet, it doesn't matter. Lasers will shoot both.
And even if it was a good idea for some reason, you'd send troops on a shuttle, not a fighter. We're talking about fighters here.
"They can maneuver through thick asteroid clusters, which would cream a big ship"
WRONG. I've already posted a link to this website, but I'll post another one to this specific page. See the Initial Idea bit. So unless you plan to duel it out in the rings of Saturn, this advantage is moot.
"A small ship can can be carrying troops, guns, or sensors that a big ship can not bring to bear"
WRONG. If the troops are for boarding another ship, I've already made my point above. If they're for planetary invasion, what you have is a dropship(a kind of shuttle) and again, not a fighter.
Apart from that, the big ship has more guns and can keep shooting for longer whether your using missiles, hypervelocity cannons, or particle beams. The little ship has the advantage with lasers because of the ease of heat dispersion for them, though, which is the only limiting factor since lasers are the only non-expendable weapons. That's why I keep mentioning missiles as the weapon for the big ship - because they don't cause any heat dispersion problems and can just be thrown off the ship with springs.
As for sensors, big ships can carry more of 'em and work independantly with their own sensors or deploy ultra-cheap quasi-stealthy sensor probes, but fighters should hopefully have something else paint the target for them because they can't afford to waste Delta-V looking for the enemy. That "something else" could be a big ship, a sensor probe, an orbital space station, or an asteroid/moon base.
"Fighters also have one important thing that big ships don't. Heat dispersion."
Valid point. But this only gives them an advantage in laser weaponry use, since missiles, charged particles and kinetic slugs are all expendable while photons are not. The big ship can carry a lot more expendables, but it has a problem dealing with waste heat from lasers. Fighters don't have this problem. The fighters' atmospheric wings can also double up as heat radiators, yes.
"What happens if you run out of missiles? What happens if your missiles are countered"
You either get outta dodge, or you get in closer and keep fighting with HPV cannons/particle beams/lasers. Missiles have the most range, so they're the opening volley.
"Drones are versatile, can be reprogrammed, and can be rebuilt"
Ultra-minimalist disposable sensor probes make better scouts, although they only fly in a straight line or in a slowly decaying orbit. Their minimal heat output makes them much harder to detect too. As for rebuilding and reprogramming, you can do that with missiles and probes too.
"You won't trust drones to paint a target."
Yes you will. The U.S Air Force does it all the time. Predator may be remote controlled, but Global Hawk is an autonomous bird. Not to mention unmanned(="drone") satellites.
"Drones are fun until you realize how STUPID they are."
Stupid? Hell no. It's manned fighters which are stupid, putting severe, massive, hideous and downright ridiculous penalties on their accelerative and maneuvering performance because the stupid human body inside can't tolerate it despite all that tech you put in there to pamper it. And you lose people when they get destroyed. Drones, computing, robotics and AI are rapidly advancing technologies, and by that time, they'll easily be able to severely outweigh any advantage you get from keeping a person in there. Semi-autonomous remote control is a much better option as long as the controller is not too far away. If they are, you can always fall back on the autonomous half, the AI, which will be much smarter then than they are now.
Heck, if you compare a prototype X-45 UCAV or an X-47 Pegasus drone-bomber to an F-117 Nighthawk(which was state-of-the-art 20 years ago), you'll see that the drone outperforms the manned plane everywhere. They're autonomous and have proved that they are capable of working autonomously, but they can fall back on remote control if needed. Heck, even manned fighters like the F-22 are mostly controlled by the computer and commanded from afar by AWACS.