Why? I've just never found anything stronger than the other ships with it. It has two front-guns, which is between pyra and galleon, it's not particularly speedy, and it can't take a battering.
If you still think the Spire has some tactile edge over others in close quarters, let us know what specifically makes it superior over any other ship.
It can't take a beating, and it isn't very speedy. That is true.
However, I use the spire as a weapons platform instead of a chaser- get into a good position, and then open up. If a ship wants to ram, chute or hydrogen will usually avoid the hit. If a ship tries to keep broadsides, or simply linger at a distance with forward guns, the main gun on the Spire can disable them quickly with help from the phoenix claw. In a situation like that, it seldom matters how much health the actual ship has- once a ship's guns are down, its effectiveness has temporarily decreased, and the winner of that first volley will gain the advantage. These things can be generalized to any of the other ships in the game, though, so...
To specifically answer your question, Helmic, about tactical advantage in close quarters:
It has a short profile, but a long draft. This makes turning very easy in close quarters, but harder to follow through holes in debris.
Its fast turning speed will mean that its medium gun will (nearly) always be within arc for firing. In closer range, it is easy for ships to pass each other, and this turning speed is necessary.
At closer ranges, the Hwacha and Double Carronade are at effective range. Usually, I take the Hwacha and have that shooter take burst rounds to help disable, and because heavy clip isn't as required once we're close.
The Galleon turns too slow in close quarters, and the Goldfish's lack of an extra front gun make it less effective(Unless its a blenderfish, I guess). I believe that this ship has a higher potential DPS with its medium gun than the other ships because of this. This is also up for argument, though, but at least that's my reasoning behind it.
The Galleon, while it has more firepower and tanky sheets of armor, it is slow, and it takes more time to change position than the Spire. In wide open spaces, the Galleon is better. However, in places where maneuverability is more important, having a mobile medium/light gun combo will be more effective.
While the Pyra has two front light guns and heavy armor, it relies on constant pressure from both guns, and occasional ramming. Once again, taking out the front guns will cripple its attack power. Two light guns vs a light gun and a medium gun comes down to who shoots first and who's more accurate, but, if both weapons attack at the same time, I'd assume that the heavier firepower would win.