I have been brushing up on my Java skills this year. For 2 years I did mostly Ruby and Common Lisp development. I think that Lisp is a great research language but not so great for deployments and long term maintainability. Ruby is a great prototyping language and for small web portal projects Rails is my favorite tool. However, I keep coming back to Java because of the tools/libraries and the robust deployment software options.
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.