At the moment, the ship designs that come from medal rewards are just aesthetic. It doesn't matter which one you choose, other than the Dark Smuggler chassis. What if the designs from medals also gave a bonus? Then players would have to think a bit further that "which one do I like the look of best?" There would obviously have to be some energy cost or cooldown (akin to getting a major refit - 40 hours?) associated with chassis changes, otherwise one could switch chassis as quickly as they wanted to gain all the bonuses rather than having to plan it out.
For example:
Archon - some bonus in LM tasks (not sure what though - increased chance of LM NPCs?

)
Qpedd - Boost one section of crew by 1% (given that they are affectionate androids, they want to hang around the rest of your crew!)
Sarkonis - Boost mining output by 2% (they are here for harvest, after all)
Cerulean - some bonus against Aerlens in PVP
Lepus - Increase planetary population by 5% (Lepus artis have population boosts)/Boost scan by 2% (Wiki states "each hatchling houses unique sensing equipment")
Intruder - either a hacking bonus, or a bonus against any Sha'din NPC ship
Empyrean - Increase energy by 5% (the whole solar energy thing...)
Bane - Increase invasion chance by 5% (to a maximum of 90%)
Avenger - Gain some attack bonus against any Lazuli NPC ship/Lazuli player (one or the other)
Atlas - Increased chance of an invasion event (either temporary or permanent).
Nephthys - Gain some attack bonus against any Stryll NPC ship
Scruuge - Increase raiding by 3%
Firestalker - Gain some attack bonus against any Crimson Order ship
Vulture - not sure on this one. Maybe a bonus to planet defense? Or scan, seeing as this is awarded for alerting all types of planet...
Incubus - Increased chance of planetary invasion by 10% (to a maximum of 90%) (similar to sabotaging a structure)
Xiphos - Boost hourly artifact production by 2%
Feel free to rip apart, but constructively, not just "-1"!!

And before anyone states it, I realise that some of the numbers could be overpowered, but hey, they are just suggestions!