A couple of variables that haven't been pinned down here:
1) how large is your database (size in bytes, not # of zip files) -- do you attach files to any of your actions?
2) you say you are syncing to MobileMe with WiFi, but that doesn't really tell us anything about your network connection's throughput. What does the "Speed test" app on the iPhone (free from the Apple app store) or
http://speakeasy.net/speedtest on your computer reveal?