How do the various Pathfinder base sets differ?
In terms of system and rules all of the base sets are relatively similar with minor differences stemming from rules clarification and the system refinement that comes with the game makers continuing to improve.

The biggest differences are thematic ones, with different settings and characters for each set, for example Skull &amp; Shackles has a ship based movement system, because it's set on the sea, whereas Rise of the Runelords and Wrath of the Righteous are land based.

The similarity is evidenced by the ability to use characters from one set in any of the others. However the adventures are designed to be started with new characters, so you wouldn't want to start with a previously leveled character.