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.
I'm not the most knowledgeable on this, but in general, Clojure has smart ways to convert data types from Java types to Clojure ones. Just like Clojure lets you use functions on a lot of different data types (mapping over vectors, objects, etc), it lets you do the same with Java collections.
Instantiating objects and using their methods is pretty terse and easy when using macros like ->
Curious to know in what ways could Java interop be better in Clojure?