First of all, thanks a lot for the commentary, even the critics ^^ I would really love to make a mod adding civs whenever Civ V comes out, but rather do it in cooperation with people from the actual added civs so it can have a true historic flavour. That being said, there are some things I would like to answer:
I don't see how this is flavorful. The defining feature of Tercios is that they are a mixed sword/arquebus/pike formation. So, if they're a musket replacement, give them a bonus vs cavalry. I'd be inclined to make them a pikemen UU, rather than a musket one. And it doesn't make sense for a densely packed infantry formation to be less vulnerable to bombardment.
Thing is, Tercios were used intensively during city sieges all over Europe. I wanted to give them some useful anti - city skill other than a generic +25% strenght against cities. Also, It is hard to choose which unit they would replace since they were a strange hybrid of Pikemen and Musket. Another different possiblity would be to make them a Pikemen with a +50% bonus against infantry units: most garrisoned units inside a city tend to be infantry, and Tercios had usually the upper hand against other infantry formations of its time like Pikemen due to their extensive use of the arquebus.
Very weak. A regular granary gives +2 food free. How about instead of the +2 food, it gives a +1 food bonus to hill tiles in the city radius?
I agree, it is a weak UB and I simply think that your suggestion is better
Heavens, what is the fixation with giving naval stuff to the portuguese ? Civ games are games where land is power and the sea only is there to make space ( and I'm pretty sure that Civ V will not be as diferent as that in this ), so giving Naval stuff to a civ is actually handicapping it compared with civs that get land related bonuses.
My idea is to make sea relevant by giving it bonuses via special buildings / abilities. Also, It maddens me how horsehockey the sea is on every single civ game when compared to its vital importance during history and how utterly butt-f*cked landlocked civs are on the real life
Getting to place earlier gives little revenue by it self, especially if you can't simply buy stuff in one side and sell in other ( we can't in Civ V AFAIK ). That makes your UU little more than useless if you can't get connect conquered/settled cities to your cap, a thing that normally is done with Astronomy. We don't need a Civ V carrack, thank you.
The combination of the Nao with the special ability does give your extra revenue by getting to the place earlier. Also, you seem to forget that this civ introduces natural wonders as an extra reward for exploration, so the Nao also helps to provide with extra culture and happiness. Not to mention to be able to crush any enemy fleet 2 techs before the rivals can get even with you, which is a really nice thing to do. However, being conscious that having a naval UU sucks bollocks, I tried to compensate by the UB and SA, which I need to comment:
The UB is ok, if you change the name ... there isn't a single feitoria in Portugal and in fact they weren't meant to be in Portuguese cities You could also give XP instead of prod.... or even make it able to link to the capital even before aastro in case of offshore cities ( that would even give the benefit to making the UU you proposed somewhat more useful )
Ok, that was a miscalculation of mine: the idea was, precisely, to be able to colonize oversea lands earlier than other civs so you can start getting the benefits of the UB as soon as possible, I thought that harbours arrived with Optics too.
The SA : well, it is also very sea based to be useful Given that portuguese actually were more based in strong points ( bought/extorted to the local peoples ) scattered along the shoresd than actually colonizing remote stuff, maybe some kind of bonus in adquiring land would be more in hand.
Ok, this is a result of my poor English: when I said that the SA helped to buy sea and coastatal tiles I meant: sea tiles and
land coastatal lines. That's it, the Portuguese will be able to aquire the coastline resources faster than any other region, a la spice route.
So, in short:
Refitted Portugal:
UU -
Nao, replaces caravel. +1 aditional vision, it requires Optics instead of astronomy
UB -
Feitoria. Replaces harbour. Requires Optics instead of astronomy, overseas trade routes generates +2 production
Special ability -
Herois do mar 
Portuguese recieve a gold bonus for discovering natural wonders and ruins. Coastatal land and sea tiles cost a 75% less
-You can't make cities in the sea ( ok, very futurish )
-Naval units can't take cities in land ( very , very realistical )
... It is a land centered game. It is just a matter of degree. Also, he proposed UU will not be able to capture cities or improve land, and that is another nail in the coffin as well
Support from naval units made Civilization Revolution navies relevant again, so I don't think that it is too far fetched to think that bombardement will do the trick again for the Civ V vessels, specially considering that you can kill land units with boats. Still, the real problem of sea on civilization is that:
1- Sea tiles suuuuuucks bollocks and give almost no resources when compared to land ones
2- No realistic trade route system = sea loosing almost all its purpouse. From a geostrategic point of view, the sea is a gigantic transportation network for goods and humans.
I will comment about the Netherlands latter. In short, I really, really liked the effects of its SA, but I agree that it makes little sense from an historical POW.
. The sun started going down slowy 
for spain empire exactly at 1588 when they lost their masive army.
