I adore combat freighters bc in "the rp of the game," those are the dudes I mentally identify with (not an accident it's these kinds of ships that feature in my micro-fiction over in Lore). The problem imo is that we have some of these ships being great, and others are sorta "eh, let the NPCs use them" even if you are a dedicated logistics-enjoyer.
I love Ventures. They're a great combination of "not fabulous at anything but good enough at a LOT of things."
I love Hounds. Their cargo space is small, but put twelve of them in your fleet, and it adds up fast. Plus they're zippy on both a burn and combat level. They don't do a whole lot besides die in a straight up fight against anything in their weight class, but they're great for harassing and for supporting some of high-tech's fragile fast movers.
I love Shepherds. They're the Venture's super-baby brother and I wish we had a viable version of this concept in the middle at the destroyer weight class. Like Venture, it's master of nothing but good enough at a surprising number of things.
With respect, Buffalo Mk.II doesn't belong in this conversation -- it's a pure combat conversion with no freighter utility. With expensive upkeep and only 20 cargo storage, it's not a combat freighter in any meaningful sense of the word. It's the Tarsus->Condor conversion chain but for missiles rather than cheap interceptors. I suspect you could convert Mercuries to create a nice initial wall of Harpoons the same way (and then order them to retreat before they die, which their speed will allow). Its good OP would allow that, but its extremely limited passenger and cargo size works the same way BuffmkII does -- no longer a logistics vessel.
Base Colossus would be a great combat freighter if half those gun turrets were turned into missile mounts. Its speed and cargo still makes it worthwhile, but if it gets engaged, it's just dead (unlike Venture). It's logistics are great, though. Possibly unfair to include it.
Colossus Mk. II and Mk.III both suffer from the same problem -- those small ballistic turrets don't do much to protect their thin skins. They die very quickly to almost anything (even Hounds). Mk. II is a pretty good station-killer if you're going after pirates with a weaker fleet and can suppress their fighter/missile load.
Colossus Mk.III is pretty good as a troop transport and okay-ish as a combat carrier -- though ime as a non-optimized middling player, they die faster than either Gemini or Condor. I'm trying to figure out how to give them some love and make it work. Its fragility is bad enough that I find Gemini outperforming it consistently (but then again, Gemini is no troop carrier).
I struggle to figure out how to make good use of Cerberus. A frigate that isn't zippy is kind of a victim (though its Burn is great! 12 burn with no add-ons for Cargo Enjoyers fails to suck, a lot). So far I put flak and LMGs on it and tell it to support other stuff. Since its write-up is very explicitly that "it can survive long enough to run," that makes sense. The built-in overrides make the LP one zippy and fast for interdicting hounds, etc., without losing cargo capacity. In any longer fight it falls to pieces, but that's just a built-in part of the game disadvantaging frigates and destroyers regardless of firepower. As a horse-archer enjoyer who enjoys fast plus enduring, I don't like that, but I'm not about to lecture Alex on fundamental mechanics.
I like Wayfarer, and I want to like it more, but I almost never use it. The problem with it is its logistics is pretty much awful. 5 supplies per month (for a frigate hauling 150 cargo), compared to 6 for Base Colossus (for 900 Cargo) or 3 for Base Buffalo means that it comes in way behind on "supplies per haul" and isn't really effective on a "use it for escorting/harassing like Hound," (3/mth) bc the math fails. It's fast and stealthy-enough for zooming around doing plot-related stuff where you don't want to have a big profile, but its utility outside of that gets dodgy quickly ime.
My suggestions are actually super simple.
Wayfarer: integral efficiency package and it would go from a pretty okay ship to a real standout.
Cerberus: it's solidly okay. But since its whole setup tactically is "survive long enough to get out of combat," replace integral burn drive with integral augmented drive field, and it'd go from "it's okay" to "wow that's fabulous."
Colossi -- swap some ball turrets for missile mounts, and like the Buffm2, let its paper-thin skin stay the balancing factor, so that it's working in the same category that dedicated Harpoon enjoyers are doing, but at the Cruiser weight class. That would make all three variants.
