Large hanger compliments with a small defense fleet set to engage locally inside a mass of repair platforms and turrets will do a number on those siege frigate fleets.  Siege frigates get weighted very small in the firepower matchup, so it's easy to present the ai with a losing situation they will run from, even when they can kill the planet.

dont spam bombers vs siege frigs,

always keep armor types in mind, fighters do alot more damage vs lrf's, siege frigs and bombers

whilst bombers are meant to take out most of the remainers

90 Siege Frigates must be goddamn'd expensive, in both credits, resources, and fleet supply.

They get torn apart by Fighters though. Fighter squadrons deal 19-22 DPS(depending on faction) each to siege boats, and carrier cruisers and hangars can pack 2 or 3 squadrons. That's serious damage raining down on those flimsy pricy trinkets that have no self-defense capability.

Phase Jump Inhibitors will screw 'em if they try to run, and you can milk experience points from the dying siege boats to level up your capital ships present in the system.

Did I say 90 Siege??  It was more like ...120!  No, it must have been...150 Siege!  Yeah...it was 150.  What are you gonna do then, huh?  Huh?

1.  I don't think you got attacked by 90 siege.  Unless it was from about 5 AI's at one time.  Or you are adding up the siege from multiple attacks.

2.  Build more defenses

3.  Split your God Fleet up a bit and leave a little on defense.

4.  Go destroy the enemies worlds with your superior fleet, an eye for an eye.

Late game i tend to get 20 or so siege crafts , thats a rough  number .

Guys, he's playing the AI.  A long game against them without cornering their fleet gets you one hell of a siege frigate mass.  90 is not an unreasonable number for him to be running into.

Kole, you didn't list command cruisers.  They are quite useful, get them in equivalent numbers to the repair cruisers.

Cataclysm, TEC can play the AI with just capital ships easy, Advent too.  The ai is too braindead to get past the Dunov shield restore tactics, although he has way too many Kols and way too few Dunov's to make it stick.  He can still butcher less than game ending fleets just fine.  The fleet is near perpetual with half that many capital ships too, if you hate reinforcing, it's the only way to fly.

Ok...sorry...I have just never seen this many siege....ever.  But I admit that I stopped playing the AI in epic multi day games many months ago.  If the AI is building these types of fleets, you can try making packs of carriers with fighters to do hit and run attacks on them.  Siege isn't real fast, and you should be able to inflict a lot of damage on it with some raiding.  Just use a scout first to locate teh siege pack and make sure it is safe for carriers, and run the carriers if help comes.  Better to fight the siege in some other system than wait for it to come to yours.