There is a mod that makes Hero ship size bigger (HeroCommandShips). This mod uses the teck tree to unlock a bigger hero ship size, the only cost is the time it takes to research the teck.
Currently in game the Heroes typically max their skills out at level 37-38 depending on the hero skills they have.
I'm not much of a modder so that is why I made this a suggestion I would like to see this as a game mechanic rather then a mod.

Suggestion:
Part 1:
I would like to see something like the HeroCommandShips mod but the heroes have to unlock the new ship with a new skill that all heroes have.

The skill would unlock after 4 skill points have been used.

First unlock:(Cost 1 skill point) Advanced Small size hero ship. Adds 1 more module slot on it (determined by ship class).

Second unlock:(Cost 2 skill points) Medium size hero ship. Adds 2 more module slots on it (determined by ship class).

Thrid unlock:(Cost 1 skill point) Advanced Medium size hero ship. Adds 1 more module slot on it (determined by ship class).

Fourth unlock:(Cost 3 skill points) Large size hero ship. Adds 2 module slots (determined by ship class) and 1 large attack module. The large attack module on hero ship well not take the Core Cracker weapon.

Fifth unlock:(Cost 1 skill points) Advanced Large size hero ship. Adding 1 module (determined by ship class) and 1 large attack module.

Upgrading the ship to the new unlocked size cost Dust and some strategic resource. Just like upgrading your fleet, or changing modules on the hero ship.

Part 2:
Add another hero skill that unlocks after 16 skill points have been used.

This skill starts off costing 1 point and increases by 1 in cost every time you add to it, but maxs out at lvl 6 so it takes 21 skill points to max out. [(1+2+3+4+5+6=21) the cost of each skill level]

Each lvl on this skill adds a special all in one module to the hero ship.

Can only and 1 special modules to small ship size, 3 to the medium size, and all 6 can be added to the large ship size. So even if you unlock all the module skill level but have not unlocked or upgraded you hero ship you can not add all the modules to the small or medium hero ship size.

This well add another 29 levels worth of skill point usage to each hero, and well add a total of 13 modules and 2 large modules to the hero ships

Total hero levels needed to fully max new skill tree 68-69 unlikely to ever get that level (it's hard getting a hero to level 40 in 200+ turns).
Total hero ship module count:
Small: 8 + 1 special + 1 if size is advnaced = 10 modules
Medium: 11 + 3 special + 1 if advanced = 15 modules
Large: 14 and 1 large attack module + 6 special + 1 and 1 large attack module if advanced = 20 and 2 large attack modules.
Making hero ships mind blowing, and giving the ship more ability in battle.