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My understanding is that the "optimizing database" step was there all along, but only recently has the time spent doing it been made visible. There is also a bug that causes it to be done inefficiently (most noticeably when you have a lot of transactions that have yet to be compacted in the history) for which Omni has an unreleased fix undergoing extensive testing. I don't know about you, but I would rather they take the time to make sure it is solid than ship something now that speeds the process up but causes database corruption in obscure cases!

You leave the iPhone or iPod running some app or another all the time when you aren't actively using the device. Cultivate a habit of having OmniFocus be that app and you won't spend as much time watching that progress bar before they ship the fix. Also, the quick entry button works during the optimization process if you are in a hurry to add something.