This is more just my personal opinion than a bug or anything, but is there any chance you could boost the spawn rate for higher-end frigates on the Citadel worlds? Some of the best ones, like the Conduit or Aural, I've either never once seen for sale -- or they're so rare I never manage to find one until I'm past using frigates fleets and am already primarily using cruiser-based fleets. Don't know if this is just me or I'm plain unlucky.
Also, maybe consider nerfing the Stable's fuel capacity? I play several mods, and with the exception of tankers and that one phase frigate from vanilla, no other frigate-class ship has more than 80 fuel cap. At 150 fuel cap each, the few Stables I use for carrying loot or cargo also mean I never need to use tankers. The Stable already has a nearly 50% cargo advantage over the next best small freighter, so the huge fuel cap on top seems like it's going from awesome ship to outright overpowered. Maybe consider two variants of the Stable -- one that has nerfed cargo for its higher fuel cap, the other which keeps its current cargo.
And possibly bump up the initial purchase cost (or, its upkeep cost via logistics or crew requirements). As I mentioned it carries 50% more than its nearest competitor, but if it has almost identical purchase cost and upkeep cost, there's never any reason to buy any other small freighter besides the Stable.