Dan,
If you're considering making fighters the same as ships, why not open up some of the other aspects of fighters as well?
E.g. Range of weapons, fighters within fighters (missiles), ECM, stealth, etc. I know I know...the math would be lovely.
As far as the voting goes, I have an effect in mind that I would like to see. I'll leave it in your good hands to determine how it's implemented. I'd like to see escorts (i.e. small ships, not fighters) to have the ability to intercept seekers just by getting in their way. Kinda like how escorts would take the hit from torps vs capital ships in WWII.
Speaking of torps, it would be cool to see fighters that can't be shot down at all...whatever description this may take. Perhaps they fly "underwater" through subspace? Again this may be redundant if fighters could have stealth, ecm, cloaked, etc.
Last request, I would love to see this trait (or something along these lines)....
Suppressable (*0.X): If the flight is targeted by a number of shots equal to half or more than the flight size, the flight cannot attack this turn, regardless of how many of the attacks actually destroy fighters in the flight.
I think that trait would go a long way to getting some value from investing in a little bit of anti-fighter tech. Otherwise, taking a few flak type guns hardly seems worth it when the ships are getting overwhelmed by fighters. It's also cool to imagine pilots screaming "There's too much fire! I can't get a line in!"...before they fly back to base.
Finally, a word of caution. Despite my obvious love of fighters, I worry that fighters are the one aspect of the core system that can be abused. A mass of little ships is generally balanced against two huge capital ships. But a mass of fighters? I think it starts to become roshambo, depending on how much anti-fighter tech the capital ships have. And so far you've done a really good job of avoiding roshambo.
I never tried to take a fleet of all independent fighters, but considering my group's collective love of the Starship-Exclusive trait, I think it would have raped the galaxy in our campaign.