The primary measure of the player's skill is Accomplishment Points, also known as Fame Points. There seem to be a maximum of 126 of these a player can achieve in his career before time and health force him into retirement. Points are awarded for cash banked and land acquired in grants from governors (which plays no role except in scoring), for total rank (first military then noble) granted by each of the four nations (even Spain, aka the Bad Guys), for Named Pirates defeated (not final rank on the Ten Most Wanted list), for their buried treasures found, four points for each of four lost family members found and progress towards rescuing them, four points for each of four lost cities and progress towards finding them, and up to 10 for finding the hideout of and defeating Montalban, the big villain.
One interesting thing about the system is that no attention is paid at all to the difficulty level through all this. The player may begin a game at any of five difficultly levels, and when crew dissatisfaction forces him to end a voyage (which always happens eventually, although finding a lot of loot can delay the process) he may choose to advance (or lower, if he didn't do well) the difficulty. Increasing the difficulty makes almost all aspects of the game harder, but is traded off in that the player's share of the treasure at the end of the next voyage will be larger, up to 50% on the hardest level. But besides wealth points acquired (and it's not hard to build up wealth), difficulty level plays no role in the primary measure of the player's achievement.
As time passes and the player's pirate ages, he periodically loses health. He begins at Good Health, and passes through Fair, Poor and finally Failing. I believe that, when the player hits Failing, the current voyage will be the last one, but I've only played one full game so far so I have no real proof. There seem to be a couple of items that can be acquired that help preserve health, but even with both of them my first game ended at the age of 48, after a little less than 30 game years. I had 92 points after all that, on my first real play through, enough to get the penultimate rank, Bishop. (The highest rank is Governor.)
As a voyage continues, over time, crew morale progresses from Very Happy to Happy to Content to Unhappy to worse. The instructions say that eventually a crew will mutiny if the player doesn't voluntarily end a voyage. Plunder acquired can raise a crew's mood back up a step temporarily, but the longer the voyage lasts, the less of an effect this will have. A couple of items, a couple of the specialist crew members, and having a relatively low number of crew members each can help delay the inevitable, but all voyages must end eventually. Playing at higher difficulty levels also makes crew members lose mood faster.
Despite the lowering of morale (which affects many things in the game, not the least of which is proficency in combat), it is in the player's best interest to delay ending a voyage for as long as possible. The longer the voyage the more loot he'll get to put into savings towards his Wealth Score, the more cash will go to each crew member for his share of the loot (making it easier to acquire more crew members during the next voyage), the longer before the player will be forced to acquire a new crew, in a sense starting from scratch again, and the longer the player will get to keep all his items (the manual claims on higher levels, some may be lost between voyages). But the most important reason to delay ending a voyage is that at least six months (and I've seen as many as eight or nine) of game time will be lost each time, which is rather a lot.