My wife and I both consider Puerto Rico to be the best game we've played so far.
So it would be reasonable that we would try the 2-player variant -although it took us a while.
Anyway, to the game:
I started as Governor, since my wife picked corn, and after a few seconds of thought I began the game by choosing the Settler and taking Quarry.
From early on in the game, my wife had a Craftsman-Captain strategy, mainly focused on producing corn and sugar and shipping them like crazy, going for the direct VPs.
I on the other hand -as I usually do- went for money, producing few Indigo and much later in the game Coffee and selling them using the Trader.
As far as the building went, my wife started with a Small Market, a Construction Hut and a Hospice all built before round 5. While all I had to show was a Large Market and an Office (as I said going for the money).
Moving on in the game having collected quite a few Doublons and also having 3 Quarries, I built a University, a Harbor and a Factory while producing 1 Corn, 2 Indigo and 2 Coffe. My wife on the other hand had 2 Quarries, produced 5 Corn, 2 Sugar and 1 Indigo and sneak-built a Wharf, leaving me with the Harbor as I mentioned before.
Two rounds after my wife built her Wharf I made the biggest mistake in the game, she had played Craftsman and had 6 Corn, 3 Sugar and 1 Indigo lying around, while I had 3 coffee, 1 Corn and 2 Indigo. On the 6 space ship there where 2 barrels of Coffee and in the 4 space ship 2 Indigo. So happy enough I played Captain so she could throw it all in the sea, completely forgeting her Wharf! As a result all I did was collect 8 VPs (due to Captain and Harbor) and my wife 6 VPs.
Later on my wife built a Small Warehouse to keep her sugar safe and quite early (since we always used to leave large violet building for last rounds) she built the City Hall. So I had to built something for my people and chose a Residence since I had 10 out of 12 fields occupied.
Another "punishment" for not paying attention was that the Craftsman hadn't been played for a round and the Captain for two. The 6 space ship had 3 barrels of Coffee and the 4 space one was empty. So my wife chose craftsman, produced her goods, then I went on to choose settler to fill up my island, completely ignoring the ships. So when my wife chose Captain I loaded the 2 barrels of Coffe that I had and threw 3 barrels of Indigo and 2 Corn! By then my wife must have had about 34 to 40 VPs while I only had 20-something.
Then my wife, started choosing Mayor much too often so that she could end the game and did. At that point I valued my University, playing as my last action a builder and choosing the Customs House mainly to cut of my wife from a lot of extra points. Which she noticed and wasn't very happy about!
Final score: Me:63 - Wife:59
So I got the University, the Customs House and the couch!