I prefer AI and campaign change over stat change any day, and changing how ship fundamentally work I think it's a hard task to do, maybe force every ship to have Hard Mode hullmods that change flux, CR, and Ammo to make it easier to program but how the AI will handle it? It's already had a hard time with certain ship, the only solution probably making the ship design even simpler to make the AI behave more intelligently. Long range laser glass canon builds will be meta since you deal more damage and the enemy cannot even reach you thanks to the Advanced Targeting Unit and not rewarding player who make SO or more dangerous build. Not to mention how it will change the lore surrounding it.
IMO Starsector taking the right decision here, the game have no difficulty options, making everyone have the same upside and downside, and Iron Mode as default mode in the future release. Making it more immersive since you're nobody after all, you will fail as everybody else, what matter is how fast you carry on.
If you want you can try Ruthless Sector and Starfarer Mode, it's more or less make the game harder without fundamentally changing anything, for example having 10 capital ships is no longer viable because how little money you make, supplies and fuel will kill you first, in a way it's already changing the fuel and supplies economy. And fully upgraded colony is an open invitation to the invader because everybody hates you more and the faction you aligned with. Both make the game harder without cheap stats changing or multiplier.
Nexerelin
https://fractalsoftworks.com/forum/index.php?topic=9175.0Ruthless
https://fractalsoftworks.com/forum/index.php?topic=15279.0