[ianbetteridge]

20 minutes is an exceptionally long time, and may indicate that the Omnifocus database on your desktop could do with a bit of spring cleaning. Try using the "Rebuild database" option (under the File menu) and also possibly moving old data to an archive (also under file) and see if that speeds things up. Even if it doesn't, it won't harm things :)

To answer your second point, yes, you can use direct Mac-to-iPhone sync via Bonjour instead, and it will be a lot quicker. If you only have one Mac, this would actually be my preferred option. However, if you have more than one Mac (or for some reason more than one iPhone!), MobileMe or WebDAV is the best solution.

Hope that helps.