CivLucas, a big post and I apologise up front if this sounds pushy or something, I don't mean it that way at all.
I have been thinking about this since I started posting. I really enjoy the East Indies mod and probably play it more than any other mod I have downloaded. I don't know if it "needs" improving, but I have wondered if you would be interested in adding the Japanese and Pacific islanders as natives. I know the Portuguese were active in Japan very early in the period as well as the Dutch. Japan was a major source of income for the Portuguese and brought high quality finished goods like silk and porcelain into the European markets. The Catholic Church ( especially the Jesuits and Dominicans ) was ( were ) interested in the Japanese as a potential military force to combat the growing Protestant menace in Europe and as a invasion force to displace "heathen" states and powers in India and Asia, and made numerous attempts to Christianize the Japans until they became such a threat to the Shogunate that it resulted in the Closed Door policy with only the Dutch having access.
By the 1800s the whole of the Pacific basin was partitioned where almost every rock that stood above the tides was being used as a depot to refresh water supplies and repairing sails and masts for shipping lanes. Later these became coaling stations, but that's outside the time frame of the game. But even remote places like Rapa Nui (Easter Island), the Galapagos, and Wake Island became important to the Europeans. Many places and technologies that were formerly vital became unimportant after the excavations of the Suez and Panama Canals, for example Yankee clipper ships lost their importance when the Panama canal opened. After the opening of these two canals, only those powers that were in disfavor with the powers controlling the canals had to use the older routes rounding the Horns of Africa and South America, and that became a mere inconvenience after the development of steam engines and stabilizing gyroscopes.
As arkham4269 points out, pirates in the East Indies were always a menace to trade, even today we see it on the news. I have seen the entry in the Civ Info XML for barbarians, so I have wondered why they have not yet been harnessed as sea faring marauders. Even if all they do is sink ships, it would add the "danger" element that is largely lacking from the game's transportation of goods. The reason the European powers built large navies wasn't to wage war on one another, although they did quite often enough, but to protect their cash flow from the West and East Indies. In fact, I have often wondered why it is that the King doesn't simply impound any ship you send to Europe when you refuse a tax increase. If he has the power to refuse to trade a commodity with you and cut you off from Europe altogether, why not confiscate all your goods until you cave in and say yes? Hell, why do you even have a chance to refuse a tax increase until you declare independence? The historical colonies certainly didn't have this choice presented them LOL
Pepper, nutmeg, cinnamon, cardamom, and other spices of India, East Asia, and the "Spice Islands" were the main economic cause for initial European interest in area. Spices were a virtual gold mine for the European powers and even the Germans became involved in both missionary and colonization efforts - albeit late in the history of European colonial effort.
Cocoa (not coca), coffee, and then tea became fashionable and even addictive substances in the European market - each commodity developed a "coffee house" cult in its turn, leading to the importation of vast quantities of cocoa beans, coffee beans, and tea leaves into the European and colonial markets. The upshot of this was the establishment of cocoa, coffee, and tea plantations being located in any region with a climate suitable to the cultivation of these goods.
Latex and rubber were curiosities but became important commodities by 1820 or so, but that's too late a date for interest in historical game play. However, opium poppies which incidentally are native to the Mediterranean basin, became a crucial economic commodity fairly early on, resulting in opium plantations being established in many places. The native demand for opium due to addiction displaced the rum trade early on and became very lucrative, even crucial to the economy of the European powers in the East Indies.
Hemp also played a vital role in the economy of the time, being an absolute must for durable sails and ropes, displacing cotton for sails by 1650 in the Asian trade zone. Hemp became so important a commodity in the age of sail that hemp cultivation became globalized and hemp plantations were established every where the European powers went.
So I have wondered if there is any chance of having spice, cocoa, tea, hemp, and opium added as commodities to the MORE YIELDS module. By the 1700s you see pineapple, sugar, and tobacco being introduce in the East Indies, but largely sugar and tobacco are anachronisms in the East Indies, so a simple substitution of opium poppies with its finished good being opium could replace the sugar/rum commodity and hemp with a finish commodity of rope could replace tobacco/cigars.
Tea is maybe more historically important that either coffee or cocoa, but it could be added in a manner similar to that of indigo and coffee since it really doesn't under-go much of a "finished good" process.
I have already added Hawaii and Samoa to my install of 1.3 and it hasn't unbalanced the game play, but I am uncertain which personality and traits really are best suited to them. I'd like to know what personality and traits you'd think would make them work best with your design. I'm working on Japan now, what I'd really like to do is have the Japanese be like they are in Civ 4, a stone wall of diplomacy, rather than the suck-ups all the natives seem to be in the vanilla game engine. LOL