Right now, SBT + IDEA is a bit of a pain because they share the same target folder and IDEA sometimes overwrites/deletes .class files that your application (started via sbt run) hasn't loaded yet. Usually that leads to a few ClassDefNotFound errors and such.
Hopefully that'll go away once we have a single SBT instance.
My two wishes for SBT would be: 1) A monadic style for .scala build files. It would make dealing with the immutable bits of project definitions so much more pleasant and we could avoid the weird semi-Scala syntax of .sbt files. And 2) A bottom-up approach similar to Pants. My team frequently end up getting a lot more project interdependencies than we bargain for simply because it's too easy to induce transitive dependencies.