Ok, I have a couple of simple solutions to some problems. Feel free to chuck 'em out the airlock if they sound too flimsy.
If a hex in Leviathan is 75km, and a typical battleship has an acceleration of 2 per turn, then that equates to 30km/m in accel. There's a real world measurement that you can incorporate into the data displays. The only thing to keep in mind is that the game will have to be able to handle however many different ships with their own acceleration rates.
Regarding intertia-based movement. It sounds like maybe you haven't played Freespace? I don't know. But . . . assuming that you haven't, Freespace is like X-Wing and Tie Fighter in that fighters and ships have a maximum velocity. They're either stopped or moving up to their maximum speed. Their maximum speed can then also be boosted by use of afterburners. Ships tend to range in speed from 10-50 . . with most warships being 30 or less. Fighters/Bombers start at around 45 and go upwards from there . . with top afterburner around 170-180 maybe in FS2? So giving a Battleship for example a speed of 30 m/s, and consequently some DDs might be around 75 m/s might be a little fast. Everything is relative though of course. The fastest fighter in Leviathan looks to be the Arcubalista at 13 thrust . . . so 13x15 = 195 m/s might be a little fast. But maybe not, would have to try and see.
But, for intertia-based movement . . . I know some people have sorta done some tests where their fighter had unlimited speed limits but I'm not sure how well that worked. I've never really heard of the AI having those same sorts of movement . . . especially the ship classes. It would be worth looking into but I'm not sure that it's possible. And if it is possible, how would the AI handle it? And would it be fun for the player?? These are all questions worth looking into.
Bay weapons may only fire in a single direction, requiring the ship be steered for targeting outside the arc the weapons cover. The broadside bays may not fire forward or aft without turning the ship either left or right. The forward and aft bays may not fire into the broadside arcs. They count as a single shot, regardless of how many guns are in the bay. If the bay takes damage, then the firepower is correspondingly reduced until the bay is useless (say three of four glancing strikes or a single direct hit).
In Freespace there are basically two types of weapons on ships. Turrets and hardpoints. Hardpoints by their very nature have a fixed arc of fire so they'd work well for the bay weapons. I'm not sure that a weapon can be reduced in effectiveness through damage. One work around would be to simply break up bays into smaller bays. Say if you have a 100 gun bay, make it into four 25 gun bays instead. This then poses the problem of "bays can only fire at one target". If the guns are beam weapons, the player creating the mission can script the weapons to fire at certain times at certain targets. If they're projectile weapons, I believe that the new FredOpen mission builder allows a player to give weapons priority targets. Basically so that non-beam anti-ship weapons fire at ships instead of trying to fire at fighters. This target priority would ensure that each "bay" even if broken into smaller sub units, fires at the same target. The only thing is they probably wouldn't be firing at the same time.
The one thing I don't recall seeing mentioned was power allocation. The ships engines have to supply power to more than just thrust and weapons. . . . As an emergency measure, he can divert his life support power into the mix and make a fighting withdrawal with all of his functional weapons fully powered and engines in overthrust. Of course, this may have a detrimental effect on the crew, and if the crew dies of asphyxiation, then all the power in the galaxy is not going to allow that ship to survive.
This has more to do with mission scripting rather than game mechanics. Aside from the players craft, ships don't have power allocation. But for capital ships for example the mission designer could script this sort of thing into the mission. For example, one option in the mission designer is to "lock-turret". This prevents a weapon on a ship from firing. A person could for example, "lock" several weapons when one of the ship's engines is disabled. The mission designer could link all of the weapons to one or more of the engines, such that when the engine is disabled the gun ceases to fire. I know that some people, I believe Trashman for example, like to "turn off" weapons on ships as they become damaged whether they are destroyed or not.
The sense of desperation you describe can all be communicated over the comm channels, as it was done in Freespace2 on occasion.
I like the idea of fighters being able to target specific items on a starship's hull. Sensors, weapons and engines stand out as BIG targets in my mind, with other possibilities easily making the list. If they can take out the engines, then that would qualify as a kill, since the ship would be without power to fight or escape. Taking out the sensors makes weapons targeting and even target detection harder. And, of course, taking down the weapons bays or turrets degrades the ship's firepower. I like the idea of making the hangar bays capable of being destroyed. It also comes to mind that, if possible, the Leviathan ships have two sets of drives. The T-space, and the normal space drives. Damaging one or both may not actually kill the engines. But you could certainly prevent the ship from manuevering or escaping.
You can certainly add "subsystems" onto a model and have them be relevant to the mission. Ships typically have weapons, sensors, navigation, communications, reactor, fighterbay and engine subsystems (plus associated turrets). Of those, fighter bay is not targettable. I'm not even sure if there's any effect on the ship for any of those, though I know weapons supposidely decreases accuracy. But a modeller could add the T-Space drive for example . . . I don't think fighterbays are typically destroyable, but I think a person could add say a "hangar entrance". All fighters have conditionals to entering the field. If you have say two wings of fighters leaving a Frigate, you could have a conditional which effectively says "as long as hangar Entrance is not destroyed". So when the hangar entrance subsystem is destroyed, they stop arriving. But typically you can't destroy the fighterbay.
But basically a lot of what you want can be achieved through the design of the mission. The behavior and stats of the ships only go so far.
Let's say for example you have the player trying to help capture a ship.
You could have them first destroy the T-Space Drive subsystem . . . if they don't the ship will eventually jump out, if they do the ship will just keep running under normal engines.
Then the player has to take out the engines, and linked to each engine is a number of weapon bays and turrets throughout the ship. Once the engines are all down, the guns cease firing. And the allied transports can come in, dock and deposite the marine assault force.
For destroying subsystems like turrets, etcetera certain weapons can be weighted towards being more effective. Weapons have three values in freespace, damage versus shields, versus hull and versus subsystems. If you give a weapon a good anti-subsystem rating it can destroy the engines more easily.
