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Before Lion, the only choice for developers was a free update or a new version of the app that everyone had to buy (just as it works in the iOS store). Lion now supports in-app purchases so in theory the update could be done with an in-app purchase, but that presents a number of issues that make it more difficult to write the app.

Updates through the Mac App Store do need to wait for Apple's approval so OmniGroup could release them sooner for people who bought directly.

Since the OmniGroup has always offered reasonable upgrading pricing on their other apps, I've purchased all my OmniGroup apps directly from them (and it saves them Apple's 30% cut).

I'd be curious to hear their plans for how they're going to handle major version updates, but I suspect they're not ready to make that decision public and they may not have even made the decision yet.

At this point, I think it's safer to buy directly from them, but that's just my opinion (and I don't work for OmniGroup).