I seriously think that Uncharted Waters: New Horizons (SNES/GEN) should be considered one of the greatest sim-RPG's out there (Bear with me action fans).
Also be cautious, there is a poor PC version out there. A port that the charcters wouldn't purport to port in.
The game revolves around one of six characters that the player gets to choose from at the beginning of play. Each has a unique story and a penchant for a certain style of play. These scenarios give you a nice story-driven way to play through the game, but the beauty of UW: NH is how you can shy away from this and embrace a very open-ended simulation experience if you so choose. You can even defect to any of the other 5 nations once you gain a title (be careful, though... this influences the country's attitude toward you).
Here's a look at the personal stats page:
You maintain your ship (which includes custom-fitting its cargo space, setting ration levels, hiring crew, equipping guns, etc), build a fleet (through fair purchases or hostile takeover), and hire officers from around the world as you sail your way to fame.
The main ways of gaining fame and money are three-fold.
First, there is trade. Get a crew together and find what goods are best to be purchased and sold at what ports. Each port around the world has different exchange rates on products, and its own set of goods to sell. Markets adjust to inundation, and sometimes you have to sail quite a ways to find just the right deal. Ports can also be converted to your homeland's territory if you put enough money into its economy. However, enemy merchant fleets likewise influence the market (if you choose to care). Guilds in most ports offer jobs to the casual sailor also.
Secondly, battle. Join up with your country's navy and patrol the seas for pirates or an opposing country's fleets. Guard your merchant fleets and raid others. Or get a letter of marque from your regent and go pirate on the seas... with free reign to plunder as you please. Assuming of course that you can take out your target. Battles between fleets are turn-based, and make use of every ship's manuverability, firepower, and manpower as you move them along the section of sea that you engaged your enemy in. Furthermore, you can try to duel the opposing commodore. Be sure to equip proper armor and weapons (found in weapon shops (rare ones in exotic places)) before engaging. Your skill is translated into a set of move options (a level of power with a type of attack: 1-9, lash/block-slash/dodge-thrust/parry).
Third (and my favorite), you can become an explorer. Roam the seas around Africa, Asia, or South America in hopes of finding native villages from which you can discover treasures or great landmarks. As you sail, if you have the cartography skill, you fill out your world map. Report your findings to get rewards from your financiers. Be sure to grab rare goods and ships from foreign lands, but be careful not to linger too long. Your crew may grow restless.
This great game offers so much replay value I have yet to get bored of it, and it is easily one of my 10 favorite games of all-time. Once you play it, you'll realize just how shallow Sid Meyer's Pirates really is. I can't stand to even touch it.
Also somebody should have said Suikoden 2 and Shadow of the Colossus by now. Don't make me write on those, too.