I am having the same problem. Syncs are now taking well over two hours to complete the "backup" process on the iPhone. I've never been this frustrated with an Apple product. I think disgusted is a more accurate term. They have done absolutely NOTHING to even address these issues publicly since the launch. This phone feels like it's running beta software, at best.
Wait for firmware 2.0.1? I shouldn't have to "wait" for anything, nor should any other users. If Apple would take five minutes and at least acknowledge that there are major sync issues with firmware 2.0, maybe most of us would feel a little better, but they don't even bother to visit their own forums and offer support advice. I suppose we could all flood the Apple stores and demand that something be done, but what would they do? Most-likely they would simply restore the device and call it a day. Even if they replaced the phones, that wouldn't help at all, since there isn't anything wrong with the phones themselves.
I have about 550MB of apps installed on my phone. This is NOTHING in terms of size and Apple should be able to write their software to deal with this much data, and a whole lot more. These full backups every time I sync my phone are the product of lazy coding, period.
I absolutely love Apple, I've got several of their products, and I've never been this upset with them in the past. I'm willing to accept a few bugs in firmware 2.0, but making my phone useless for the better part of two-and-a-half hours is pathetic design. I'm telling my friends not to bother updating to firmware 2.0 on their original iPhones, and to hold off on getting an iPhone 3G (like I did) until Apple gets their act together and does something meaningful to address the issues we are having. These are not isolated issues. Far too many people are having the same issue and it's far too easy to reproduce.