Games

You might like Horizon's Gate.

I've never played Sid Meier's Pirates! but if you've ever played Uncharted Waters: New Horizons for the SNES, it sounds like Diet Pirates! Trade routes, mapping the world, discovery of exploration sites on the shore (lost cities, tribes, etc), ship and captain battles (and some small RPG elements in character progression and story). No weather systems, or real city growth. Trade will effect prices of other trade goods in a port, and you can flood a market, so you have to rotate where you're selling between a few to let markets recover.

Anyway, Horizon's Gate takes all of that stuff from UC:NH, expands on it a little bit, adds Final Fantasy Tactics style on foot combat using your crew. FFT style equipment, classes, levels, abilities, can mix and match when you reach a certain job level.

Actual RPG style dungeon crawling with the ability to use party combat techniques during on foot exploration. Freeze water to cross moats and rivers, electrify magitech equipment in abandoned labs, use your jumping attacks to cross gaps, burn away overgrowth to get through jungles to lost temples, use the floaying movement tech to get over pressure plate traps, etc. Reminiscent of Golden Sun in that way.

Basic crafting system where you can use different materials with unique effects to make different weapons and armors, then slot in gems to further augment properties.

Ship equipment with passive effects and different ship weapons with different effects, including magic cannons that can do stuff like freezing tiles so boats can't pass them or wind cannons that blow other ships around.

Can have multiple ships in your fleet with different specialties.

Kingdoms with different specialties, unique equipment, unique ships, and unique character classes that you can pledge to and do various quests and research stuff for to earn kingdom favor.

RPG style rumors in town that can lead to dungeons and little side quests, mysteries, and the like that aren't always tracked.

Not really weather "systems", but there are things on the overworld like headwinds, roving sea monsters, stuff that can give similar sorts of effects I guess.

Graphics obviously inspired by SNES era Final Fantasy. To the point that I'm pretty sure there was some tracing.

And a small but deep and impressively well polished modding community with a lot of really polished additional content. More randomly generated and hand crafted dungeons, more classes, settlements, questlines, recruitable characters with character specific stories and dialog, expansions to existing systems, entirely new gameplay systems and elements that almost always blend and interact seamlessly with each other and the base game.

With all the different ways to customize character builds and equipment, there's a ton of depth to combat and a lot of ways you could probably make overpowered setups. Unfortunately this game has taught me that I suck with this combat style. I use a mod to give me two or three extra crewmates than you can normally bring into each battle.

So... it wouldn't have the same depth for the sailing, city building (outside of a few modded questy towns), or weather systems. But it's a fairly unknown indie game that I can't reccomend enough, especially if you like Final Fantasy Tactics.