We just have Khan saying that Marcus dreamed of a militarized Starfleet, and that Vengeance is one of the few ship designed solely for combat. That makes it sound like a ship like Enterprise could have been made alot stronger. Not that it could beat a battleship, but that it could have been a much stronger cruiser than it was, and that this non-militarized Starfleet is somehow holding back on the combat capabilities of their ships.
Thats becuase regular Starfleet ships have science labs, and explorationy things in them which need space which means less room for more guns.
The Vengenace being a purely combat design does not have any of these exploration based things and as such can fit more equipment for combat stuff especially since its twice the size of Starfleet's newest heavy cruiser class.
Presumably Starfleet would have warships though. Khan makes it sound like only a fanatic militarist and war monger like Marcus would think it useful to have ships designed to fight.
Of course ships can be designed to be multirole. Convertible spaces for different equipment, etc. But the implication is that Starfleet mostly makes ships weaker than they could make them. And have virtually no warships of any kind for self defense. Instead, these weaker science and exploratory ships have to be the ones to fight off invasions and other threats. That's hard to believe.
It's not hard to believe at all. 99% of the things that try to attack Federation planet can't be repelled with military solutions. The Federation gets attacked by giant space amoebas, vampiric cloud monsters, planet-eating nebula beasts, flesh-eating pancake things, and we've seen whole solar systems threatened by hyper-evolved space probes and two separate occasions. In alot of those situations their tactical systems are actually the
least useful thing on the ship; most of those threats are dealt with through careful deconstruction and a liberal use of science (or Kirk yells at them until they self-destruct).
Really, the only time Starfleet ships even use their weapons is to defend THEMSELVES when some asshole starts shooting at them. Otherwise, the most important place on the bridge of a starship isn't the weapons console, it's the science station.
STID is actually the ultimate proof of this. Vengeance clearly outguns the Enterprise to the point that Marcus initially curb-stomps them in lunar orbit and should be able to finish the fight in less time than it takes to eat a bagel. Even after Khan takes over, it's not even a fair contest; Enterprise is no match for Vengeance. And yet, Enterprise WON that fight. Not by out-fighting or out-shooting Vengeance, but by coming up with a creative solution and exploiting Vengeance's many weaknesses: First, it's excessive reliance on automation allows it to be easily sabotaged, and second, the fact that that the man flying it is is a lunatic.
You've confused Starfleet's reliance on scientific research and data collection as "weakness." Don't worry, it's a common mistake (just ask the Klingons).
I read somewhere they were torpedo launchers. Marcus' line also supports this:
MARCUS: I'll make this quick. Target all aft torpedoes on the Enterprise bridge.
They're not. Vengeance's main armament is actually a type of projectile weapon that's designed to physically bypass deflector shield sand punch right through the ship. Basically, it's a railgun from hell. The turrets that fold out from the bottom of the ship would have been this if we actually saw them fire; they're basically one-shot kills.
Vengeance's aft torpedo launchers are... well, torpedo launchers. Not that unusual except that like most of V's weapons they are hidden in armored silos in the ship's hull.
Timo is totally on point here. Those torpedoes are presumably designed to be on par with at least a tactical nuke -- 50-100 kt, say (I would wager more -- an 'isotonne' is a made up unit, so I prefer to work with real numbers). A 1 kt nuclear blast will basically take out everything within a 400m radius. That distances scales up with the cube root of the yield. So, figure the explosion of a single one would cripple anything within 1 km of the blast.
Set 72 of them off at the same time? Inside the ship? No shields? It ain't just going to blow out a few walls....
If you actually look at the test footage of nuclear tests conducted in close proximity to naval vessels, it's not as overwhelming as You'd think. Granted, those ships aren't CONTAINING the blast the way Vengeance is, but even at distances of only a few hundred meters, it's not as if they're being vaporized outright or smashed to bits either. A nuclear detonation in the multi-kiloton range is very impressive against things like wooden houses and shacks, but even concrete structures will stand up to a nuclear detonation at relatively close range.
And Vengeance is a starship specifically designed to contain blast damage from a torpedo hit. The interior design undoubtedly has interesting features -- anti-spalling layers, energy-dampening materials, internal forcefields, shape-memory alloys, etc -- that allow it to contain some of the energy from a penetrating torpedo hit. Even if the torpedo imparted all of its energy in a hard x-ray flash like a nuke (and there's zero reason to believe it would) the initial fireball from the blast would be JUST large enough to push out through the hull of the ship and then the overpressure would dissipate uselessly into space, which is more or less what we see in the blast.
If I'm honest, though, I don't think torpedoes compare well to nukes. Starfleet has the technology to create forcefields and control gravity; a radiation bomb is beneath their capabilities. Whatever it is a photon torpedo warhead actually does, it only needs to do it within a set radius large enough to encompass the hull of most starships. It IS, in fact, going to blow out a few walls (or as many as it can in a given radius) because "blowing out walls" is the worst thing you can do to a starship and is exactly what a photon torpedo would be DESIGNED to do.