This isn't exactly unprecedented, but there's been some discussion about "upgrade pricing" regarding Logic Pro X today, so I thought this would be good info for Logic Pro customers. First, if you bought Logic Pro within 30 days, consider contacting Apple support -- you may be able to get a refund (within a week). With that money you can happily upgrade to Logic Pro X through the Mac App Store.
As for the upgrade pricing for customers beyond 30 days, I'm not sure why that was ever a mystery. When Final Cut Pro X debuted, there wasn't upgrade pricing, either. Logic Pro X continues the Mac App Store practice of no upgrades from purchases made off the store. In a short amount of time it won't matter, as pros will have purchased the update through the MAS anyway. Unless Apple creates another version currently on the Store that requires a separate purchase also from the Store -- but it hasn't done that with any of its apps thus far.