Well, if you're just playing with people you know, it doesn't really matter. However, these are the rules typically used in 5v5 PVP games (the most popular competitive format in Sins for whatever reason).
* Quick Start
* Standard Fleet Sizes
* Fast game speeds
* Pirates Inactive
* Locked Teams
Basically the settings are designed so that games finish as quickly as possible. Usually there are no formal victory conditions applied, but once a team gets a clear advantage the losing team is expected to quit so that everyone can get on to the next game as soon as possible. Since the teams are picked in advance, they are of course locked. Pirates are typically seen as a distraction, and partly luck based which is a bad thing in any competitive game.
Of course, if you're just playing for fun use whatever settings you like.