I noticed something when in a recent battle. On the Omicron Alpha side (mine), several large ships (a Outcast Dred, an Outcast Destroyer, and a Hessian Cruiser), a Greyhound, and me in my gunboat. On the invader side, there were three or four VHFs and an Albatross.
On the side with mostly fighters, the Albatross went down first. Really, really fast. All the big ships concentrated on it and ignored the fighters until it was destroyed.
On the side with mostly capital ships, the Greyhound went down first. I forget whether it was before or after the Albatross got taken out. A fair while later, my gunboat was taken out.
See, this is the problem with vastly unbalanced fleets. If you're the only big ship in a group of smaller ships, you're taken out first. If you're the only small ship in a group of larger ships, you're taken out first. Trying to take out fighters in a big capship without the use of missile turrets (and many capships don't bother with them, because there are better guns available for fighting other capships) is bloody difficult. I'm pretty sure my gunboat had a much easier time hitting the fighters than the cruisers and destroyer (though at the time I had four VHFs ganging up on ME, so a fair amount of my effort went towards keeping moving).
A group of fighters has no chance against a group of capships, but they can be darn annoying. Likewise, a group of capships (with the possible exception of groups of gunboats or ships with lots of missile turrets) aren't very useful against fighters. They're speedy little buggers and really hard to hit.