The game really doesn't need new ships in Skirmish. When you add another ship, you add more balancing issues. Other ships get nerfed or buffed to counter it. Usually nerfed sadly.
The better option is bringing in the upgrade system from Alliance (It isn't implemented yet). This is a PVE mechanic designed to enhance your ship. Originally it was said it would be PVE only, not PVP, but it wouldn't be a stretch to make something like it work for PVP. I've been doing a lot of Steel Ocean recently and they have something like this where you spend silver (which you don't have to pay to earn), to get upgrade parts. Some are straight upgrades where others are tradeoff upgrades where you gain 10% of something at the cost of 5% of something else.
How would this work for GOIO? So lets take for example the Nerfmidion. Say we give it, 3 upgrade slots. Each slot you either unlock by playing (level requirement) or matches drop in game coin that can be used to upgrade them. Then you have your upgrades, could be obtainable either way as well. Taking Steel Ocean for example, lets say the three upgrades used are: Armor - 10% HP for 5% speed reduction, Improved engines - 10% acceleration buff, Better rotors - 10% turning improvement. Suddenly Nerfmidion is not so crappy anymore.
Now those are just examples. The possibilities of other upgrades are many. Could tailor some to pilot tools or even to damage types. Say you are facing a munker and would like some passive form of protection against impact damage. It wouldn't be much help but there could be an impact damper that reduces the impact effect. Heck if fire is a problem, could do a upgrade that slowly puts out fire stacks. Maybe 1 stack per minute or something. This upgrade system could also possibly be done on a character level.
How this system would fail, is if it was just given away and everyone could use it from the start. This is Blizznomics and their "content for everyone" approach that has afflicted many MMOs since Burning Crusade. When you give away items or dumb down content and don't give something to strive for, you might as well shut your game down. People need something to strive for, something to make them want to put in the time and effort unlocking. There needs to be a sense of accomplishment. Provide that, even if players bitch and moan, you've got a winner.
Sure this would mean upgraded ships would potentially be outclassing regular. But so what. As long as it's not by a large amount, its fine. Give people reason to want to level up and play. So they can be the upgraded vessel. In Steel Ocean the upgrades are so marginal that you really can't tell who has or doesn't have them. I put a turning upgrade on one of my subs and I could notice the change, but it still wasn't enough to make me super OP. There are upgrades that enhance part durability. These are virtually impossible to tell who has them unless you fire directly at the part and even then, it'll break eventually anyways. This could be done as well for GOIO. Shatter resistance could be added. Just make it low enough where it would provide a visible benefit but not invincibility. Or make it for individual parts like SO does. Say engine resistance. Squid pilots would rejoice as their engines are so weak and easy to break that even 10% better would be welcome.