In my opinion choosing a different language than the host (in this instance Java) has to bring enough advantages to balance out the disadvantages, like less (idiomatic) libraries, less documentation, less tools, less developers available on the market. Not to pick on Kotlin, I'm sure there are people that love it, however I personally don't see what advantages a language like Kotlin brings over Java 8, being CoffeeScript versus Javascript all over again. With Clojure or Scala we are talking about languages going into territories that Java will never venture into, for the simple reason that Java is designed to be mainstream, which really means appealing to the common denominator. Of course, as we've seen with CoffeeScript, the market can be irrational, but it started to go away already, after a new version of Javascript plus the realization that everything brought by those small syntactic differences was bullshit.

Going back to Clojure and the need or lack thereof to recompile call-sites, given that Clojure is a dynamic language that doesn't have to concern itself with much static information and that does get distributed as source-code, I feel that this is an apples versus oranges discussion. But anyway, lets get back to protocols. So protocols do generate corresponding Java interfaces, just like Scala's traits. Except that Clojure being a dynamic language, there isn't much to do when your functions look like this to the JVM: https://github.com/clojure/clojure/blob/master/src/jvm/cloju...

There's also the issue that Clojure's standard library has been more stable. Well, that can be a virtue and in the eye of the beholder can be seen as a good design, however it has many things that need to be cleaned out. As a Clojure newbie I couldn't understand for example why I can't implement things that work with map or filter or mapcat, or things that can be counted, or compared, only to find out that its protocols and multi-methods aren't used in its collections and that there isn't a Clojure specific thing I can implement to make my own things that behave like the builtins. It's also disheartening to see that the sorted-set wants things that implement Java's Comparable. Clojure's collections have sometimes surprising behavior - like for example I might choose a Vector because it has certain properties, but if you're not careful with the operations applied you can end up with a sequence or a list and then you have to back-trace your steps (e.g. conj is cool, but the concept should have been applied to other operators as well IMHO). Transducers are freaking cool, however I feel that the protocol of communication isn't generic enough, as I can't see how it can be applied to reactive streams (e.g. Rx) when back-pressure is involved (might be wrong, haven't reasoned about it enough). As any other language or standard library, Clojure is not immune to mistakes and personally I prefer languages that fix their mistakes (which I'm sure Clojure will do).

EDIT: on "separate compilation", not sure why we're having this conversation, but generally speaking Scala provides backwards compatibility for everything that matches Java. Adding a new method to a class? Changing the implementation of a function? No problem. On the other hand certain features, like traits providing method implementations or default parameters are landmines. Along with Java 8 things might improve, as the class format is now more capable. As I said, there's a roadmap to deal with this and with targeting different platforms (e.g. Java 8 versus Javascript versus LLVM) through TASTY, but I don't know when they'll deliver.