There are two main problems I see with large capital ship in an FS-verse setting
Number 1 is Mission Space - the standard model of FS combat designed about is around an average speed of 65 m/s and highly linear movement which means you get a mission space that is spherical from the starting point with a max radius of about 65 * t(mission time in seconds) - that's a radius of 58.500 m for max space if the player only moves linearly in one direction for 15 minutes without maxed afterburner (mission with a mission time above 15 minutes become increasingly unwieldly from a balancing standpoint, just on the ammount of time you spend running iterations to make balance solid). However, your player will not be going flying straight somewhere for 15 minutes, so the sphere generally shrinks dramatically - I usually get it down 20.000 unless something special is required, like 35.000 when reaching an point is actually a mission objective.
Having a ship that is entire lenght of that radius is means that you have going from one point to another on the ship might take up the entire space of the mission. Not to mention that the geometery of the ship might force you to fly certain paths, combat maybe forced into certain avenues by the enemy arrival positions and turret fire - which would contract the maximum space. Having the ship take up that much space also means that if it is the point of the mission to interact with that ship, you have to start to contract the space between the locations of the individual task into only a small section of the ship, which then requires a few logic pretzels to resolve (e.g. doing a "trench run"-scenario) or you wind up defeating the purpose of that ship size.
All that can be altered if you make your ships faster (higher average speed means more space), and introduce support ship hull repair or regerating health for the player (means you get to extend mission time). Another idea would do tactical jumps, but then you have to deal with the impact of the overall logic of the campaign (e.g. tactical jumps make the world of the story feel smaller because it forces the task on small group of actors).
EDIT: Note all figures are purely theoretical - most of the time (esspecially if you cut down mission time to 8-12 minutes) they tend to be much less.
Number 2 is general problem that the base model of FS capital ship interaction always has the "damage over"-trap door - because of how ship-to-ship and bomber-to-ship combat is established, it runs on a logic that shooting at thing enough will always make it explode; FS1 had introduce the Lucifer's unique plot shielding to get around that, FS2 flipped that in High Noon by making a point on how "just big guns the thing" was bearly working as a solution.
To desing the mission about a ship of large size, you have to respond to the logic of why the mission exists when the trap-door "just shoot it enough" is still existing.
While you can do some amazing solutions to that problem using SCP mechanics, e.g. armour types, and destroyable subsystems - but by the time you are finished that and implimented it across the board for consistency and training players to use it, you basically have turned the systems of ship-to-ship combat into something new.