CYOS is a very focused mod, providing a very specific set of functionality. As such, there are a few other mods users may be interested in as a supplement to CYOS.

This is specifically for things related to ships, mind. Not a full list of every mod I use, ain't nobody got time for that.

Balance Mods
Realistic Fuel Cost: Tier 9 Cap. I like Realistic Fuel Cost, but because of how CYOS was implemented, costs would get absurd. Thus this mod.

Mechanics
Crew Capacity Configurator allows you to set your crew capacity on a per-character basis. So if you build some massive dreadnought, or use the Fregata, you can have a small village there if you want.

Aesthetics
Avali Colored Items Addon: Holograms & More. A good choice if you want your Avali to fly a ship of a different color, but you still want to bring some Avali flair to it. The required Avali Colored Items may also be of use in that.

Better Ship Animations. Because honestly I just hate that stupid turn.

bk3k Blocks and Objects. While none of this is really ship-specific, having some block-based sources of light can help with the BYOS capsule, to get light to places it may be needed without an obtrusive light object.

Engine Blocks and Cables, because every good ship needs an engine. Unless you're using, like, solar sails or something.

Hull Plating Blocks and More offers a lot of ship-specific items, making it another excellent supplement for the Ship Construction License in CYOS.

Maxthechosen's Wall Panels are actually more in the style of the vanilla ships, but can be good for detailing on those.

More Sloped Blocks really is quite self-explanatory. The base game didn't give a lot of options in that field.

Placeable Dynamic FTL Drive, for similarly self-explanatory reasons.

Xb's Materials adds some more heavy-duty-looking ship components, great if you want a more industrial look to your ship.