The Mac App Store makes it impossible to charge for software customers have already paid for? Tragic.
You can emulate upgrade pricing via bundles.
If you sold V1 for $5.00 and then you want to sell V2 to new customers for $5.00 but existing customers. You can bundle the two versions for $8.00 and in the description for V1 you tell them that version 2 is available and don't buy it. You tell customers that have bought V1 already to get the bundle for $3.
But if you ever want paid upgrades or you are already a well known app -no.
For instance it wouldn't make any sense for MS or Adobe to be in the Mac App Store.
Ben Woodruff
AgileBits