This should be easy to fix with a 'configure my controller' option. They could let you choose which keys do what for their game, and maybe show the most common configurations as options before you make your own.
If you take the Flash market as an example, any sort of configuration seems to be too much effort for most developers to undertake.
(Although I happen to be building a Flash engine that would simplify adding configuration options.)
That's just laziness or lack of foresight on the part of the developers, adding customisable keys should be trivial.