They are very specialized for the most part, and cannot perform all of the same roles that other ships can do, "acid sprayer", so they needed to be treated as so. Personally I think all bonus ships should have different research requirements due to thier overall effectiveness....Yes someone can say they are all decent, but there are some obvious advantages to having another 200 laser gatlings compared to a handful of chameleons, cost should be equated to how easily they can be induced into the blob mechanic of the gameplay, if they are specialized, make them cheaper.
The problem in this case is that the cost problem is not metal/crystal, which I think is what you are implying. The biggest cost problems of getting a useless ship are the entirely finite resources, and then the one you value more preciously in real life.
Cost 1) Knowledge. It is finite per game. This is tied into AIP being precious. 3k knowledge is 20 AIP (at least). 6k to get mk 3 is 40 AIP. You can't get that AIP back (data centers don't count because those are ALSO finite and act as an AIP reduction cap per game, not a resource. the resource spent to get that reduction cap is time though). The cost of a mk 3 ship is more or less 40 AIP. If the power of the ship doesn't justify +40 AIP, you don't get it.
Cost 2) AIP. You spend 20 AIP just to take the planet. If you wanted the mk 3 ship ANYWAY this is a non-factor because you would have just taken a different planet to get the 20 AIP of knowledge.
Cost 3) Time. It takes time to take the planet. It takes time to get there. It takes time to harvest the knowledge. It then takes time to leave if you're not staying. I assume you are going to die at some point and/or have to work sometimes, or just get bored of the slog, so this is important.
Cost 4) Everything else you didn't unlock instead. If something else is better, you should have unlocked that instead.
If too many ships are too narrow in scope, the chance that all those prices you pay are wasted for no gain increases, or at least not a comparable one. Ideally, all ships would be worth at LEAST +40 AIP in ANY situation and better than default unlocks in most situations, but can then be better in a more focused manner beyond that. For optimal gameplay, many people are probably way undervaluing AIP assuming my math and experience with non-floor AIP are correct.
Nukes are an example. Nukes are never worth their AIP unless you're screwing around or entirely desparate for an instant kill of stuff about to blow up your HW you can't stop. A useless-for-your-game-situation ARS ship can't even blow up an entire planet in a pinch.