Before I answer the question about the $x.99 pricing, let me address another logical fallacy. Apple is not raising prices for EVERYONE. Apple is raising prices for those publishers and/or authors who choose to use Apples service, and who choose not to lower their prices instead of raise them.
Now, on the the $x.99. I don't work for Apple, so can only speculate. But don't think of it as prices that end in $0.99. Think of it as their iTunes connect app management pages refer to it, as tiers. You see, by limiting the amount of possible prices, they are able to set and keep set consistent pricing across the world, where currencies are not the same. $1.99 USD may be 1.45 currency X dollars one day and 1.56 currency X dollars the next day. Of course, they could always display the prices in the native currency of the content provider like Android does. Nobody ever complains about having to run to a currency converter program to figure out exactly how much they are paying for the latest and greatest fart app, right?
The fact is, Apple has that pricing structure for a very sound, well thought out reason. One that benefits consumers in a way that competitors like Android fail them. It's why Apple has the market share that they do, and why you are all riled up that you have to play by their rules. You could very easily not publish on Apple platforms, but you want the market share. The market share that the very things you complain about help to build.
