What's different in San Juan's second edition?
Artwork and the following.

The Prefecture now costs 4 instead of 3.
With the Goldmine, you now get to keep the cheapest card instead of any card.
With the Guildhall, you get 1 point per production building and 1 point for each different production building.
New building Hut: "In the trader phase, the owner of a hut draws one card from the supply if no good was sold by any player during this phase." 
The Bank now costs 3 instead of 4.

And yes this is a copy paste from BGG, if you don't want that please explain how BGG didn't fully explain this.

Link: https://boardgamegeek.com/thread/1330934/differences-between-1ed-and-2ed