I think I'm going to comment only on things that surprised me.
Astral in S-tier? I haven't used it in a while, but is it really as good as death god Radiant? I really doubt it could stand up to Radiant, except maybe with all the skills and player piloted, maybe.
Your description of Ziggurat is a bit confusing me; do you not know that motes can attack ships and EMP them through shields? It makes it the best dueler in the game, since if the other ship isn't shooting at you, you win flux war by walkover. It is a logistic nightmare, though, and merely a bigger Doom.
I'm surprised Fury is just B-tier. I would have easily put it in S-tier; not because it has amazing absolute stats, but because its stats for its DP are indeed brilliant. It's like having 2/3rds of an Aurora for half the price (that's 50% more Aurora per Fury than Aurora per Aurora!). You can make an endgame worthy fleet of just Furies.
I wouldn't put Drover in A-tier, but mostly because its ship system is a fighter replacement suicide button (except maybe with skills and EDC?) and that carriers aren't so good anymore.
Brawler in S-tier? Whoa. It's just a long range distraction. That's decent, but not S worthy.
Wolf in A-tier? Once it runs out of missiles, it's only a distraction. Maybe it's worth something with woofpack tictacs, but Tempest is worth a lot without that, and gets even better with that.
Omen is easy A-tier to me (it's point defence, anti-fighter, EMP, mad efficiency in one ship system! Distraction, cruiser-level shields, support, all in one ship!), since on top of respectable combat capabilities it's useful on campaign layer, too (though that one I can guess you aren't taking into consideration, just the combat capabilities).
I've heard Scarab is about Tempest power level (sometimes better, sometimes worse), but I haven't bothered to try it out.
Wayfarer not in the bottom tier? lol