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A nice consequence of simple file syncing based on modification date or version is that it doesn't matter what's in the files, thus Omni could "easily" put the same sync engine into their other iPad apps, like OmniGraffle.

OmniFocus has to be the gold standard for syncing but the downside is that the approach requires all clients to read/write via a complex proprietary file based transactional mechanism rather than just having to cope with a simple flat file.