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.
PS - You may already know this, but you can change IntelliJ's compile output directory [0].
[0] - http://www.jetbrains.com/idea/webhelp/configuring-module-com...
About monadic style: I realize that it's a hard sell, but it's basically about leveraging for comprehensions (aka. do-notation) to specify your build. Shake is an example of this, although probably not particularly suited to building Scala code.
If you are looking for something faster and more declarative, you may want to check out SBT[0]. It is way faster than any of the other JVM build tools. Also, in the future[1] it should have much better tooling support than anything else on the JVM.
[0] - http://www.scala-sbt.org/ [1] - https://github.com/sbt/sbt/wiki/Client-server-split