Worker Placement

You need at least one worker in Regions 2 and 3 most of the time, as the building actions here are vital to winning; and in the forest. Region 1 is less important, since it has only one building to activate, unless your strategy depends heavily on colonists (in which case, move them there as soon as possible to maximize the number of rounds they can produce).

Region 1:

Alfândega (Customs): If you have workers in Region 1 this building action can be used to earn an extra PP for each of the player's ships in a particular colony, in addition to the resources gained during Phase D for each colonist. This strategy works well with the Expeditions Crown Request.

Region 2:

Moinho (Mill): A reliable end-of-round source of 5 bread, if you have 3 workers in this region.

Capitania (Captaincy): The main way to move workers into the city. If you have 3 workers in the region, you can earn an easy 15 points over 5 rounds.

Region 3:

Casa da Coroa (Guild Palace): Important once you have accumulated guild favours.

Fortaleza (Watch Tower): The most powerful building on the board; it is a rare round that you will not want to place a guild die here. Placing one or two workers in the City Watch accomplishes 3 things simultaneously: discarding pirates, enabling you to use pirate die, and scoring 4 VPs if you have a majority in the Honor phase.

Getting and Losing Pirates

Plan to have no pirates at game end: otherwise, the potential 16-VP swing may cost you the game. To play optimally, however, you will need to take pirates in order to conserve money, bread or wood, then discard them later. That said, try not to leave yourself with more than 6 pirates at the end of a round.

The main way of discarding pirates is placing workers in the City Watch, via Fortaleza or other means (Scout, the 3rd passing favour, the King's favour). All these actions discard 3 pirates (or 6 if you activate Fortaleza's stronger ability). Therefore, especially as you approach the endgame, make sure you have an even multiple of 3 pirates. (Constable allows you to discard half your pirates; it is the only exception to the rule of 3.)

Putting a guild die on Fortaleza (if you have workers in Region 3) lets you skip paying for an earlier building action, then discard the resulting pirates at Fortaleza: a very efficient way to conserve money.

Bread

Never start a round without bread, as you need it to modify dice. Take a few pirates if necessary to hang on to some bread.

The Windmill

Do not neglect to use the Windmill to trade goods, gain bread, etc. Whenever you can, especially early in the game, move up the Windmill to conserve bread. (The Miller guild favour is especially useful for this.)

Passing

More actions is not necessarily better: try to pass early, once you've completed all actions you absolutely must do. Unless you urgently need an action lower on the passing column, grab as high a spot as possible. Consider taking the 2 reals to guarantee first pick of dice, request, and guild to unflip.

Crown Requests

When selecting crown requests, consider whether they work well together, what round you will fulfill them in, and what requests will be left unclaimed for future rounds. In general you want to avoid ending up with multiple copies of the same request in Round 5, as the 2nd copy will usually score little or nothing.

Urbanization (city workers) is the most useful request, in Round 1 especially, as you are guaranteed to score some points with no effort, and scoring 12 or 15 is relatively easy.

Wealth of the Nations (money) is poor in Rounds 1 and 3, but better in Round 5; money is too useful before then to waste on it. At game end it effectively nets only 12 points maximum (since 15 reals = 3 points), the lowest maximum of all the requests.

Influence of the Guilds can yield 15 or 20 points in Rounds 3 and 5, the highest potential return on a single request.

Market Routes and Expeditions both score up to 18 points. But avoid having to fulfill them simultaneously in Round 3 or 5; the wood/money upkeep on 6 ships simultaneously in play is onerous.

It is helpful to have complementary requests in hand: Market Routes + Wealth of the Nations (trade routes get you money); Influence of the Guilds + Urbanization (claiming Guild favours clears space for urbanization).