After reading all the posts that were created in this thread, I decided to make my own opinion. The portuguese empire should be related to trade, expansion and naval stuff. I think it should have less trade bonus but more expansion bonus (the portuguese were better explorers than traders)
MAIN IDEA
Leader: João II
João II (or John II, but we have Pedro II instead of Peter II) was one of the most important ruller in portuguese history. He designed all the lines necessary to reach india and some people say he knew or had an idea of America. He assigned the Treaty of Tordesillas giving portugal the ability of colonizing Brazil (THE major colony in the 4th dinasty until the early 19th century) and discovered much of what became (centuries after) the African portuguese colonies. But, more than that, he worked with espionage (Pêro da Covilhã) and kept all the new discoveries to himself. He worked in order to create a centralized state and finish with the feudalism that was in portugal from the origins. If I have not convinced you, he was the greatest opponent of Isabela of Spain. They were the most powerfull rullers of Europe in their time but, of course, they were not friends. When João II died she said "Murió el Hombre" (=THE man died). She used THE and not A, giving him credit for his awsom rule. And people, if you are not convinced, you know the book of Maquiavel, "The Prince" right? Well... João II IS that "Prince". He is João II, the perfect prince because of the bopok of maquiavel (and in the 15th and 16th centuries, the ideas of Maquiavel were not considered bad but good, because of the fragmented fedual europe). Do we have any better?
Capital: Lisbon
No need to explain why...
Ability: The Fifth Empire - Trade rotes between two different continents provide a 
bonus. Renaissance and Industrial naval units are 15% cheaper. A Golden Age 
begins upon discovering all the city states.
The Fifth Empire is like a mith in portuguese art used as a theme in works like "Mensagem" (Fernando Pessoa). It was first talked by a portuguese priest who lived in Brazil (they were portuguese) in the 16th century (if i'm correct) called António Vieira. He used some lines from the Bible to prove that the portuguese were going to be the fifth great empire in the world (after Babylon, Persia, Greece and Rome). The true is that some years later, portugal became part of Spain for many years. In the 20th century, in "Mensagem", Pessoa used the Fifth Empire (Quinto Império in portuguese) in a different concept. Portugal was going to be the fifth great cultural (not phisical) empire in the world after Greece, Rome, Europe (some people who study Pessoa say that Europe means England) and Christianity. When he died, the first steps of an opressive government and 50 years of ignorance and fascism afected the country. Nowdays, Fifth Empire or Quinto Império is a symbol of the portuguese culture, arts, history, music, language and everything thet defines the country as a civilization (or a distict part in the western civilization). The Fifth empire did not become a large empire with many lands or a cultural empire with the innovations in art and culture, but, after so many years, the portuguese diaspora became the FIFTH EMPIRE.
Unique Unit: Nau - ,25
5
, replaces Privateer, is available at astronomy but has the "extra sight (1)" promotion instead of the Prize Ships. When the Nau is grouped with a cargo ship or an embarked unit, the Cargo Ship or the embarked Unit have the same movement points as the Nau.
This unique is already considered by almost everyone as something that will, certainly, appear. There are 2 points in here:
1) Will it be named Carrack or Nau? We have Feitoria and Not Factory in CivIV. Plus the brasilian UU is called Pracinhas (Portuguese word, used in brazilian portuguese and not much in european portuguese, still is a native word). We have conquistador, for instance... I don't see why can this unit not be called Nau (the word Carrack is not even used in Portugal).
2) Will it replace the privateer or the caravel? Well, the Caravel was invented by the Portuguese. It can be used by every empire in civV (good) but removing the caravel from a Portuguese civ is worse than removing the conquistador from spain. Is like removing the idea of crown from the brittish (I'm exagerating, but you can see the point). Now, if the Nau does not replace the Caravel, it replaces what? Firgate or Privateer? I think the privateer is less important in portuguese history (and in the game).
So, the Nau was a large ship (comparing it to the Caravel) that had major importance in portuguese expansion and establishment in foreign continents. If portugal had an important role in european history, it was due to the naval engeneers and the advanced naval science...
When the Portuguese found the Indian ocean, they started to fight against many islamic cities in the coast. They had a strong naval assault and, of course, they stole gold from the city to bring it to Lisbon. That is the reason why i choose to keep the Coastal Raider I promotion.
Unique Improvement: Feitoria - Must be built on coastal tiles. +1 . Adjacent coast tiles provide +1 . + 50% for units standing on it and +20% for naval units next no it. Can only be built at more than 10 tiles from the capital 
Feitorias (Factories in english) were like trading posts founded along the coast and were used in trade and war. They had a major importance in the early portuguese empire that was mainly a sea empire (not much land indeed...) strong in naval military and international commerce.
As the feitorias were built in colonies, there is a limit where building a feitoria in not possible.
The Symbol - Armillary sphere
The armillary sphere is a symbol both of world expansion and naval science. It is one of the moast well known portuguese symbols and is present on the flag. The Armillary sphere should be complete in order to seem different from the brazilian symbol.
Colors: ((((((((O))))))))
These were the colors of the portuguese monarchy, the aurean period of the portuguese empire (historically speaking, IMO, people live better in a republic, but htis is not the point). As the classic red and greed have already been taken, I see no reason not to use these symbols (I will be honest: when I first knew this game existed, I thought of a portuguese blue and white civ, and it seems really beautyfull to me)
ALTERNATIVE IDEAS:
Leaders:
Afonso Henriques - founder of the kingdom, first king of Portugal and the most well known by the portuguese. Conquered almost all the actual portuguese territory
Diniz - great king with the internal affairs. He stoped the conquests and started to organize the recent kingdom, creating new towns, indepenents from feudalism, developing agriculture... Basically, he united a newly conquered territory and setteled the bases for the maritime expansion (Personally, I put him in number 2, after João II)
João I - This king, first of the 2nd dynasty, reinstaured the throne after 2 years of war with Castille (Spain). He fought the Aljubarrota battle and he even started the maritime expansion and the discoveries by conquering the city of Ceuta in north africa.
Maria II - She is not that charismatic leader. But firaxis wants female leaders and she is the best choice for portugal due to the work she gave to education in the 19th century kingdom. I would put her in the fifth place...
No alternative capital unfortunately...
Alternative abilities:
By Seas Never Sailed Before - Recieve double upon discovering a 
city state. Naval units have +1 sight and Caravels are Earned at compass - the name is after a verse from "Os Lusiadas" [the main idea was from Genghis Khan]. Is focused on expansion.
Merchants of Belém - +33% from naval trade rotes. Coastal tiles provide +1 gold when they are connected to the capital. - as you can see, this is focused on trade and centralized empire, 2 caractheristics of the imperial portugal.
Alternative Unique Unit:
Bandeirante - replaces musketman. 20 3. Recieve a gold bonus when a luxury resource is discovered. Canbuild the plantation improvement. - this unit is focused on land exploration and resource exploration. Bandeirantes were portuguese captains who went to brasil to expand the borders. late, the bandeirantes became people who lived in brasil, but brazil was portuguese.
Caçador - replaces riffleman. 38 2. +10% strenght when fighting in enemy territory - caçadores are 29th century troops specialized in invading the enemy territory. They played an important role in the Napoleonic Wars.
Alternative Unique Building:
House of Fado - replaces opera house. Has no maintenance. Provides +1 
and +1 
for each wine resource worked nearby. - Fado is the national music of portugal, known worldwide. House of Fado (or casa de fados) is a place where people get together to listen music, drink and debate. Is a place where culture flows.
Alternative Unique Improvement:
Padrão - can only be built on coastal tiles. +3 . Adjacent tiles provide +1 - padrão is a mark of the portuguese passage from a certain place. It is like the feitoria but with more gold instead of the defensive bonus.
Alternative Symbol:
Cross of Avis http://upload.wikimedia.org/wikipedia/commons/d/d8/Ordem_Avis.svg
Alternative Colors:
((((((((o))))))))
