I will announce straight off that I have only played against the AI, so keep that in mind.
I have seen they AI do some good stuff with siege frigates. If they bring them with their fleet, it forces you to concentrate on them first while the enemy fleet wipes out your defenses. Having read most of the above posts, im sure some of you would ask why i would bother if they do as little damage as you claim. well, in my experience, they do a considerable amount of damage. only if your planet has been fully upgraded to the 6k hp do they not do enough damage. and that isnt always an immediate option. I've had the AI also do a brilliant strat where right after I took their planet, they sent their fleet to attack another of my planets nearby, then when my fleet was distracted, sent in 3-4 siege frigates to the planet i just took. without hp upgrade or even having had the time to build up a defense, there is nothing I can do to save that world. and most of the time i get it back, but any money i spent trying to build it up is lost.
however, I have to say that as I have attempted to use them, no strategy worked. maybe a slight success with the 'fly with my fleet and let them divide enemy forces' technique. but i also do not wish to bring back those earlier siege raids. But i would like to use that strat where i divide their forces by using siege frigates.
Proposed Fix: give siege frigates a researched ability that increases their survivability only when in groups of a certain size. say 4-6. could be different mechanic depending on race so as to benifit from any other research you have such as antimatter regen rates. eg. advent gain some shielding, vasari gain hp regen/out of phase, tec redirects damage to in system fleet. or increase their effectiveness in culture. the point being, dont make siege ships better straight up, make it so you have to do a few things and then they can be powerful. with the right research, they should be powerful, but not on their own.
Another idea, give them a power that affects your whole fleet if they succeed in wiping out the planet. this should be a buff powerful enough that if i take a fleet that is an even match for the defenses, but manage to kill the planet during the battle, i can then be reasonably assured of victory. not a damage boost, but a damage reduction.
Im also thinking that maybe its not such a bad idea to take the approach that the new structure damaging cruisers take: long range attacks. maybe make them have multi-targeting so they always bomb the planet, but can help out in fleet dps. should also be able to join fleets like normal. that annoys the hell out of me. this would remove the divided forces strat however.
another idea you might really like: give fighters an ability called Cover. they fly cover for your selected ship, reducing its damage taken and attacking anything that attacks the protected ship. So as to prevent accidently ordering off cover, remove the fighter from the empire tree or something.
Obviously, Im not proposing all of the above be added.