I successfully used Scala as prototyping language for the first time recently. It was nice. I kinda liked it. But, I will have rewrite what I did in it soon because the VM startup cost for scala is too high for what I want to do. The lack of IDE support that the OP complained about didn't really bother me as I am more a vi/kate{+vi mode} kinda guy. That said, I could definitely see how really good IDE support would be nice to have when integrating with large Java libraries.

EDIT: I forgot to mention the one thing that is nice about Java from a research perspective is it is a really easy language to work with. It's syntax is relatively easy to deal with, it doesn't have a preprocessor. Its semantics are straight forward. It has type annotations. There is a lot of code in it so you can test your research on real code bases. This makes Java the best language to conduct research on languages in. Even if it is not the best language to write it.