What changes or improvement will the Puerto Rico expansion offer me?
Short answer:  I don't like the first expansion ("The Buildings" expansion in the Treasure Chest [BGG] set), as there are only a few good buildings; I do, however, enjoy the second expansion ("The Nobles" expansion in the aforementioned Treasure Chest).  If you are a completist and want some variety, go for it, but I don't feel the first expansion adds much to the game.

Long answer: I feel that the Nobles expansion is the better expansion, as the buildings have good synergy, the Nobles colonists put a much larger emphasis on Mayoring (you replace one colonist on the ship each phase with a red Noble piece; each Noble is worth 1 VP at the end of the game and some buildings function differently if it is occupied by a Noble) and the expansion as a whole seems to try and put more emphasis on roles that might not have been taken as much in the core game.  The Nobles expansion does have a few arguably degenerate combos, though.

The Buildings expansion to me just has some random buildings with weird rules for the sake of being "different", like the Forest House and the Black Market.  There are a couple of bright spots in the first expansion, though, such as the Storehouse, Library and Statue.

The drafting rule: very much slows down the start of the game, and while I could be judging harshly, I think the drafting is a major turn-off and slows down the start of the game pretty severely.  I don't want to pick buildings, I just want to play!  

I do like the Variant 2 suggestion in the link you provided to speed up the drafting process, but I find it simply easier to say "We're playing with all of Expansion 1", "We're playing with all of Expansion 2"), or "We're playing the core game".

I'm going to cover both expansions, just for the sake of thoroughness, so you can decide if the expansion is right for you.

Cost 1

Small Market vs. Aqueduct (Expansion 1)

The Aqueduct will give you one more barrel of indigo or sugar for a large plant when crafting, but the Small Market is practically the de facto opening move and a fantastic buy; other than trying something new, I can't see why you would want to take the Aqueduct over Small Market.

Verdict:  Small Market, hands down.

Cost 2

Construction Hut and Hacienda vs. Forest House and Black Market (Expansion 1) vs. Land Office (Expansion 2)


Construction Hut is nice for getting a quarry when someone else Settles.  
Hacienda is nice for getting a random extra plantation, when you're going for the Residence or want to get plantations as quick as possible and don't particularly care what you pull.  
The Forest House allows you to take a plantation from the stack, place it face-down on your plantation area and call it a Forest; for every two Forests you have in the plantation area, you get a 1 doubloon discount (in addition to any Builder privileges and/or quarry discounts).  
The Black Market allows you to reduce a building's cost; you may discard one colonist, VP or good back to the supply and get a 1 doubloon discount, but you cannot discard more than one of each type, and you cannot have any doubloons left after using the Black Market.  
A colonist-occupied Land Office lets you buy the topmost face-down plantation in any of the plantation stacks for 1 doubloon during the trader phase.  A noble-occupied Land Office lets you discard a plantation tile from the plantation to earn 1 doubloon.


The Forest House does give you a discount above and beyond a quarry at the cost of spending 2 turns doing nothing but getting a forest; I rather just have a Construction Hut for the guaranteed Quarry.  I don't like the Black Market because you can almost always do something with the discarded good (sell it or ship it), and who wants to discard VPs?  The noble-occupied Land Office is amusing if you get stuck pulling a plantation you'll simply never use, but the colonist-occupied Land Office is a Hacienda that you have to spend an extra doubloon for.  

Verdict:  The Expansion 1 buildings are the worst of the bunch.  Construction Hut and Hacienda still probably win, although Construction Hut and Land Office isn't bad.

Cost 3

Small Warehouse vs. Storehouse (Expansion 1) vs. Chapel (Expansion 2)

Now we're getting to some actual decisions!  Small Warehouse is great when you and someone else are producing the same good, but he gets the drop on you and captains first and fills a ship up.  In addition to your one barrel kept after captaining, a Storehouse allows you to get 3 more goods (of any type), so you effectively get to keep up to four barrels after captaining.  The Chapel, during the craftsman phase, gives you 1 doubloon if occupied by a colonist, and 1 VP if occupied by a Noble.

Verdict:  All three are great.  If you have diverse plantations, I think Storehouse is actually better.  If you want a free doubloon or VP almost every turn, the Chapel is pretty tempting. 

Cost 4

Hospice vs. Guesthouse (Expansion 1) vs. Hunting Lodge (Expansion 2)


Hospice is nice because your plantations are automatically occupied when you Settle.  
Guesthouse is extremely interesting.  During the Mayor phase, you may place up to two of your colonists in the Guesthouse.  Then, during any other phase, at any point, you may move people from the Guesthouse onto any other space on your board, where they immediately take effect.  Great for getting a Big Purple building occupied at the end of the game when no one is going to Mayor again, or when you just bought that Coffee Roaster but haven't had a chance to occupy it yet.
Hunting Lodge is such a Johnny combo-riffic building.  During each Settler phase, if the Hunting Lodge is colonist-occupied, you may discard a plantation from your island.  If the Hunting Lodge is noble-occupied, and you have the fewest plantations on the board (not tied for fewest), you earn 2 VP.


Verdict:  All three are great again.  Hospice is very straight-forward and good at what it does, but Guesthouse is a really versatile building, and Hunting Lodge is really hilarious if you can stay behind in plantations, especially early in the game.  

Cost 5

Office and Large Market vs. Trading Post and Church (Expansion 1) vs. Zoning Office (Expansion 2)

Wow, still reading?  


Trading Post gives you your own Trading House, but you can't use Small Market or Large Market with it.  
With the Church, you get 1 VP when you buy anything in the 2nd or 3rd column, 2 VP if you buy anything in the 4th column.  
A colonist-occupied Zoning Office lets you pay 1 less doubloon when buying anything in the first 3 columns, and a noble-occupied Zoning Office lets you pay 2 less doubloons when buying anything in the 4th column.


Verdict:  Office and Large Market all the way.  Trading Post suffers because you don't get Small or Large Market bonuses, and Church and Zoning Office really don't give great returns.  Selling Coffee over and over again, and at a possible +2 doubloons is fantastic.

Cost 6

Large Warehouse vs. Small Wharf (Expansion 1) vs. Royal Supplier (Expansion 2)


Small Wharf lets you ship straight to the supply, as many or as few barrels as you want, but you only get 1 VP for each two barrels you ship.  
Royal Supplier lets you ship straight to the supply, and you get 1 VP for each barrel, but you can only ship 1 of each good, and you can only ship up to X barrels, where X is the number of nobles on your board.


Verdict:  Large Warehouse or Royal Supplier.  Small Wharf is reasonably costed, and if you miss out on a Wharf, it's not bad, but I think the Royal Supplier does it better, because you're going to want Nobles anyways; it only takes 5 barrels to get 5 VP with the Royal Supplier, whereas it takes 10 barrels with the Small Wharf.  Large Warehouse is great simply for how much it can hold.

Cost 7

Factory vs. Lighthouse (Expansion 1) vs. Villa (Expansion 2)

My wrist is cramping.  The Lighthouse gives 1 doubloon for each shipment (much like the Harbor, but with doubloons instead of VP).  If you have a Lighthouse and you select Captain, you get another doubloon just for being awesome.  During the Mayor phase, an occupied Villa lets you take a Noble from the supply.  

Verdict:  They're all fantastic picks.  If your opponents will allow it, the Villa.  The Villa may just be the single most broken building in the game, as an early Villa can fuel Jeweler and Chapel, plus you're getting a free guy worth 1 VP.

Cost 8

University and Harbor vs. Specialty Factory and Library (Expansion 1) vs. Jeweler (Expansion 2)


Specialty Factory gives you X-1 doubloons when crafting, where X is the number of goods of a single kind you produced.  Produced 5 corn?  You just got 4 doubloons.   
The Library is awesome.  When you take a role, double the privilege.  It's just that simple.  Think about it.
During the Craftsman phase, the Jewler gives you a doubloon for each Noble on your board.  It also counts as a large production building.


Verdict:  Library and (Jeweler if playing with Nobles, Harbor without Nobles).  I hate the University; it is way too expensive for what it does.  The Specialty Factory is nice, but I think there is more money-making opportunities with the Jeweler.

Cost 9

Wharf vs. Union Hall (Expansion 1)

During the Captain phase, before captaining, you get 1 VP for every two of the same good you have.

Verdict:  The Wharf is just better.  If you have a Large Market and the Union Hall, and you somehow keep being unable to ship anything, I could see some big decent VP bonuses there, but I much rather just be able to ship everything at 1 VP per barrel.

Cost 10

I'm just going to cover the new ones here.


Statue -- it's worth 8 VP, period.  No occupation necessary, just fork over the 10 doubloons and collect 8 VP.  Fantastic.
Cloister -- you get VP depending on how many triplets of plantations you have on your island; 1 VP for 1 set, 3 VP for 2 sets, 6 VP for 3 sets and 10 VP for 4 sets.  Tricky to use.
Royal Garden -- all your nobles are worth 2 VP instead of 1 VP.  Absolutely brutal with the Villa.


Boy, I sure hope this helps!