Java arrays and primitive types should (perhaps) be deprecated
So, I have carefully read through both Effective Java (2nd edition) and Java Generics recently to brush up on my Java skills. As a result, I completely refactored one of my medium size projects to use generics and collection classes exclusively - no arrays. Since arrays must contain reifiable types they play poorly with generics.
There are some obvious cases where not using primitive types leads to excessive object creation and boxing/unboxing. That said, I expect Java compilers, Hotspot, and the JVM in general to keep getting better and this may be a non-issue in the future.