Hi, I have been having the same problems (basically a system wide slowdown since updating to 3.0).
I just called apple care and the guy on the phone told me that I had downloaded a corrupted version of the software due to server overload.
He basically gave me two options which were;
1. Create a new user account on my mac, set up a new (and fresh) iTunes and restore my iPhone from that user account. Then switch back to my real user account and sync my now empty iPhone to my library.
He did say that he could in no way guarantee that this would solve my issues as there are still a lot of server problems going on at apple.
2. Wait. He said that he himself had not updated his iPhone as he knew this would happen. He said he would never update his iPhone for at least a couple of weeks after the update went live. When i asked him how i would know if the server issues had been solved he said just to call apple care and see how long i would have to wait on hold.
Clearly apple was aware this could happen, that it was even likely. If the guy on the phone knew enough to stay away then why did apple even release this update? Its negligent and just another example of apple failing its customers. (We all remember going through this before in the past with updates/activation and need I mention the uber-hell that was MobileMe 1.0?)
Personally i don't think this is good enough. I wouldn't be surprised if this slow down of the old iphone is just a way of pressuring loyal customers to upgrade to the new iphone 3G S, after all we know that S is something we are all missing right now!
If apple can give a 30$ itunes gift card to AT&T customers for something that wasn't apples fault i think this epic fail warrants a decent discount on an iPhone 3G S or at the very least a new update that fixes this and a hefty upgrade to its servers with a change to its procedures.
Anyway, thats my rant over and if you want to know if I chose option one or two, I'm taking two for now because i hate the couple of hours it takes to sync the 14GB of content back to my iPhone. (However apple care might be getting a few prank phone calls from me for the next few weeks.)