Operating systems and video games require more power, so obviously not done in Java. Operating systems are written in C, not C++.
More of the programming world uses Java now. Why? Because memory isn't as big of an issue anymore. Also, portability is becoming more and more of a standard.
With Web 2.0, Java/J2EE/Javascript are more widely used in the programming world. There are far more websites than there are applications.
Oh... btw...
Odds are they did it in Java for portability reasons. May not be the most efficient choice but there is no way you can outright say C++ is more widely used than Java. Especially in the Web 2.0 day in age.
I can personally confirm that you can change the difficulty to hard BEFORE completing the first mission (food crate mission) and still receive the trophy for completing on hard difficulty. Just found the last shard a couple of minutes ago :) Now to just beat the game again on good and I'll have my platinum!