Clojure's Java interop story is generally really good. Method calls are predictable and uniform. The collection types generally work both ways, rather than being a completely independent type hierarchy (as a former Scala programmer, what a breath of fresh air). Functions work as Runnable, Callable, Comparator, etc. Reify, deftype, and proxy are sufficient for maybe 98% of APIs I've worked with.

There are, however, those rare exceptions! For instance, some Java APIs literally won't work without annotations. There's just no way (last I checked) to express those in Clojure.

I don't remember exactly the nature of this problem, but I've had occasional issues with deeply overloaded argument dispatch before. Maybe it was something like "The Java API expects an object x which responds to x.foo(long l) and also x.foo(int i) differently", and there was no way to convince deftype to emit the right kind of class.

AOT is... it's weird. You want ahead-of-time compilation when, say, you want to write a Java class that uses datatypes defined in Clojure. But AOT, at least in Leiningen, tends to break stuff in truly inscrutable ways. My professional opinion is that it's haunted.