Should I expect battery life on an iPhone 4S to be significantly worse than on a 3GS?
It's anecdotal, but John Gruber (of Daring Fireball) who tends to get a lot of feedback from Apple users, suggested on Twitter that it's a problem for some non-zero percentage of users:


  
    And my iPhone 4S's battery lasts HALF a day, where the 4's battery lasted 1,5 days
  
  
  @JMoVS I know you're not alone, that other 4S users are seeing short battery life, but that's not normal. Mine lasts as long or longer.


So it sounds like you may have got a dud. If your battery life is substantially worse than a 3GS, it may be worthwhile asking to have your unit swapped for a fresh one.