Well there's the thing I haven't wrote any races in my series yet, I've only wrote what happens at Wyvern HQ and its employees so I have no race parts yet. So for race wise you can write what you wish and I will edit my story to fit it, sound good?

I think that for the Prototype perhaps we should make the regulations work in the 2048 mechanic so the ship should have a flaw in it for balancing (e.g. Pir-hana prototype)
But for special feature wise I say it can be anything, some examples could be say (feature - flaw):

Hyperthrust enabled - low shields
Own weapon mounted on craft - cannot use weapon pads
My new ship using Zone Fibre Glass could be another example
Can activate shield weapon at any time without having to use weapon pads - Long recharge time plus no defensive weapons

Depending on what advantage the ship gains from said feature should affects its penalty to. So if it likes "THIS SHIP CAN CHOOSE WHICH WEAPON IT GETS FROM A WEAPON PAD" means it should have very low firepower to balance it, and cannot choose whether it gets offensive/defensive weapons.

Honestly though I say experiment with what you want because I love creativity, make something mind-blowing if you wish