Depends on how many peeps you have, how often you go mushroom hunting, and how much food you have (remember that island events can give and take food). If you aren't running terribly low on food (or if you don't mind mushie hunting), then get your faction first.

Magic faction will help you gain tech points a little bit faster, nature will replenish the food a little bit faster... and I think there are different benefits at the end, too (I think the magic faction gets more population, can't remember straightaway - my game is off so I can surf the forums!)