I guess you didn't expect having to move your Applications directory out of the root partition? You might wanna resize that root partition of yours now that you know that the extra space is of no use hiding away in there. Rebuild the IPSW and restore while still in your early stages of 2.0, you wouldn't wanna do that after you've settled in with tonnes of downloaded apps and stuff.

With the growing amount of 3rd party apps available, I believe that 500MB will come in handy really soon. You might wanna seriously consider repwning your phone before you've installed too much Restoring your phone's backup including all the downloaded apps will be a nightmare then.

The difference then would be the amount of time required for your first sync The part I hate the most is not the syncing or redownloading of 3rd party apps, but typing in Notepad, one-by-one, the Installer Sources and names of my installed apps. With almost 40+ installed, it'd be nearly suicidal to remember which ones exactly by heart, especially the randomly selected iPhysics level packs.