The Spire's hardcounter is everything that shoots at it. No, you don't even have to shoot at it, a squid can ram it to death from up front without being shot at.
The Spire is not made to move around, since it is as slow as it is. It's tallness makes many covers not actual covers. It also hinders it from using certain routes, because it's just too tall to fit through, limiting its sneaky-ness.
Every ship can rule any map, but that relies on teamwork between captains and their crews as well as good strategizing mid-game. If you are good at these things and win with every ship than you are good pilot in a good clan/team, it does not make the ship balanced.
What is the Spire better at than other ships? A pyramidion can have the same killing power because you don't need more than a Gatling and a Mortar. A Mobula can have even more and it as well as most other ships can dodge and tank easier than the Spire could ever hope to.
It sure can have 1 medium gun and 3 light guns pointed at the same enemy, but is it enough to even out all its negatives? I think not. I would be almost ok with it if it would just be a tini tiny bit easier to engineer...
The more I think about the Spire the more I get the feeling it is just a joke ship.