The real reason is you want to run your game on the latest greatest WiiStation(tm). if it is written in C/C++ you sit down with a copy of their development library and change your code to fit. If it is written in java you port the jvm to the device. And I don't really know how hard that is(having never ported the jvm) but most people sort of balk at that step.
Microsoft thought it was easier/better to rewrite minecraft in C++ than port the jvm to the xbox. There was a big enough customer base attached to the original java version they did not want to discard it(backlash would be too huge and messy).