The fundamental difference is that Clojure gets distributed as source and not as compiled .class files. Being an interpreted language that gets compiled on the fly does have some advantages. But it also has drawbacks. Startup performance suffers, the Java interoperability story is worse, many tools such as Android's toolchain expect bytecode, etc ...
The problem that Scala has (and also Clojure, as soon as you do AOT) is that Scala's idioms do not translate well into Java bytecode, as Java's bytecode is designed for, well, Java. Therefore even small and source-compatible changes, like adding another parameter with a default value to a method or like adding a method to a trait, can trigger binary incompatibilities.
The plan for Scala is to embed in the .class, besides the bytecode, the abstract syntax tree built by the compiler and then the compiler can take a JAR and repurpose it for whatever platform you want. This is part of the TASTY and the Scala-meta projects. If you think about it it's not that far from what Clojure is doing, except that this is done in the context of a static language that doesn't rely on the presence of an interpreter at runtime. Of course, LISPs are pretty cool. And of course, you'll still need to recompile your projects, but at least then the dependencies won't have to be changed.
