I've had similar problems with the battery not holding a charge. Got my phone on Friday and had it sync'd up and running. Friday night when I went to bed, I had 78% on the battery. Got up at 6:30 Saturday morning and the phone was dead. Coincidentally, I was at the Apple store Sunday morning to pick up a new Nano and said something to the guy in the store about the battery and got the usual - is the Bluetooth on? is Wi-Fi on? - Was the screen turned off?
Well of course both the Bluetooth and Wi-Fi was on. What good is the phone if I keep having to turn them on and off every single time I need them? And no, my screen turns off after 5 min so the screen wasn't sucking the life out of the battery. And no, all the apps were turned off and NOTHING was running in the background.
This morning when I woke up, the phone was plugged in all night and was 100%. I swear, not 15 minutes later, the battery was at 91%. When I got to work, the battery was at 82% and I'm betting it's going to be damn near dead when I get off of work 9 hours later.
What really irritates me is I traded in a 3GS for the 4S and the battery on that phone was awesome - even after over two years of use. I hope Apple fixes this problem and doesn't try to duck it like they did with the crappy antenna on the 4G when it first came out.