It really does depend on the purpose you are building the given ships for.
If you are going to want to attack, you need fast ships, especially on larger galaxies. You cannot really fit much in the way of engines on your smaller ships. You can slam the next system over with fighters, but by the time your figher fleet makes it to the far side of a larger galaxy, its obsolete. For me, Medium hulls get 2 of my best engines, and everything above that gets 4 engines.
Larger ships simply beat the hell out of smaller ships, all else being equal. One poster mentioned that a large ship will often overkill on one fighter, and then get slammed by the return volly. First, even with larger ships, you will usually have more then one, so your usually overkilling at least 3 ships at a time. And assuming you have a decent amount of defense, even off type defense, your probably not going to lose all that much on the return volly. Defences count against every attack, and you really cannot pack all that much weaponry on a fighter hull.
Where larger ships really lose out is on cost. You simply must use defence to get your moneys worth. Ordinarily, its not a big deal, but it makes your ships expensive, and requires you to pursue a given line of defence tech. If your attacked by an enemy who either has strong defences to your chosen weapon type, or weapons that your defences are not geared for, even experienced huge hulls will die. And when you have lost a fleet or two of large ships, you have lost a huge investment. Small ships are disposable, and if you suddenly find your ships obsolete, its not as painful to use your fighters as cannon fodder while you rebuild your fleet. Also, If you like leveraging the bonus effects of starbases, fighters are great, since your getting your starbase bonus multiplied against the total number of ships in your fleet. If you end up going for small hulls, you can probably do well enough without putting much effort into defence, and let your starbases do the heavy lifting for that.
I only use small hulls for planet defense, and use my large ships to pulverize my opponents, primary because I want to have fast (movement 15 or better) ships by late game, since I tend to play on the 2 largest galaxy sizes. Fast ships with the eyes of the galaxy usually results in the AI being tactically ineffective. I can move my fleets in, do some damage, and when needed, fall back to one of my planets to remove damaged ships from my fleet, letting them repair for later. Though in all fairness, I can probably finish the game out with just medium hulls, since its at that point in the game when I am fighting the only AI that can stand against me. By the time I get my large or huge hulls going, its prolonged mopup.
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