So far it would appear that the way the Mac App Store handles "paid major upgrades" is to let the developer put the product out again under a different name (ie, Pixelmator 2) and set a (modest) price for it (no "upgrade" pricing for owners of the previous version).
So, for example, Lion was $30 and Mountain Lion was $20. For everybody. Owners of Lion didn't get a discount off compared to people who jumped from SL to ML.
Overall, I like this strategy, since it appears to keep prices low. I would expect that WHEN Pages gets a new version, it will be called Pages '13 and be sold once again for $15. Seems like a super reasonable price to me for what you get.
As has been the policy since before the MAS, minor updates are free.
MS Office (assuming it continues to be sold as it has traditionally, probably a bad assumption) gets updated every three years or so and you buy it at "full" price or the upgraded price ($80 or so for the upgrade, $120 for the new).