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Have a look at the OmniFocus.ofocus file on your MobileMe or WebDAV server -- select the file and right-click on it to get the contextual menu, then choose Show Package Contents. How many files are you seeing after you've synced? And how big is the whole thing?

You can use the File->Move Old Data to Archive... command to move your older completed items out of the active database, which should help speed things up. I think OmniFocus is able to read and write the individual transaction files without having to transfer/rewrite the whole package on each sync, so old stuff that isn't changing shouldn't be quite so much of a burden, but there's not a lot of memory or cpu horsepower on the iPhone, so archiving the old stuff is probably a good plan. One nice feature of the archive command is that it will tell you how many completed items there are before a given date which could be prospectively shuffled out to pasture.