How to minimize Puerto Rico setup time?
Certainly -- the trick is do all the prep work after you finish a game.  Once you are done with the game, sort everything out for the next game.

These instructions all assume you will want to take into account the 2-Player variant when sorting; if you want to ignore the 2-player variant, ignore the bullets flagged with two stars (**).

Personally, I play a lot of the 2-player variant because I have a hard time finding a third, so I have plastic bags labelled 2 Players, 3 Players, 4 Players, and 5 Players.


** For the 2-player variant, I have sorted out 2 of each production building and 1 of each purple building into one of the trays, and have the remaining buildings in a separate tray labeled "3+ Player Buildings".
** I have removed three of each type of plantation, and placed the remainder of the plantations in one of the tray spaces.
** The 2 Player  bag contains:  65 victory points, 42 colonists.  It also contains all the barrels of goods except for 2 barrels of each type (per the 2-player rules).  
The 3 Player bag contains 10 more victory points, 13 more colonists, and the remaining plantation tiles and goods barrels.


Alternately, if you don't ever plan on playing with only 2 players, the 3 Player bag should contain the base 75 victory ponits and 55 colonists.  You won't need to sort out plantations or barrels in this case.

The 4 Player bag contains 25 more victory points, and 20 more colonists.
The 5 Player bag contains the last 22 victory points, and the last 20 colonists.


If you write the contents of what the 3, 4 and 5 player bags should have, you can fill those up, and the remainder goes into the 2 player bag.

Now all you'll have to do is fish out the necessary corn and indigo plantations to determine who goes first, and you're all set.