According to my experience at least, in a 2v2 and judging by the fact that 99% of 2v2 maps are TDM.
I think it's mandatory to say that you want at least one ship that can kill an enemy by itself and do so in a reasonable time, hence why there's almost always a Pyramidion or a Junker. Those ships are solid, dependable, can take a beating and can deliver a hit when they need to due to having at least 2 light gun slots that can overlap arcs, hence pairing Piercing+Explosive damage guns on them leads to incredibly fast kills.
Those two are the backborne army of sorts in GoI, other ships are mostly utility or snipers that need close range protection.
The Goldfish can't kill by itself in a reasonable time, but is speedy and can deliver quick strikes with a heavy gun.
The Spire is a guns platform, slow and fragile, needs protection, the Mobula is in pretty much the same category, just without a heavy gun and complicated decks, works slightly different and is even more sniper focused.
Finally the Galleon, while packing a lot of fire power, still needs close range protection cause it has horrible handling, it's also incredibly weak to disabling weapons like the Hwacha, Artemis and Mercury gun.
So, depending on what you want to accomplish, you usually should be pairing a Pyramidion or a Junker with one of the other ships, or just get a Pyramidion AND a Junker, since the Junker is also suited to bear utility weapons while retaining a fair portion of killing power, or just go dual kill build and utility front.
Keep in mind that I'm talking about 'effective' team set ups, ships like the Spire or the Goldfish have problems with akward pairings. Obviously the Goldfish is an attacker ship, you won't be pairing it with a Spire since the Spire can't follow it around, the Goldfish can't protect the Spire reasonably well either, you are also pairing 2 ships with the same innate weakness, an exposed front gun, your enemy might want to take advantage of that, so it's a bad match up.
A Spire and a Junker is an example of a decent match up, since the Junker can fend off attackers with a close range side and assist a long range Spire with a long range side equiped with Mercuries/Artemises.
You can also pair a Pyramidion with pretty much everything, even itself.
Yes, I know I didn't realy post many team setups, but I want to believe this posts explains how team set ups work in a short and effective manner c: