All IME, and as a Scala fan:
Clojure has a weakly integrated type system (an inherent disadvantage of optional type systems). At the simplest level this makes silly errors much easier and means you have to write more tests to maintain the same defect rate.
The lack of types mean you require extensive use of macros for advanced functionality. IME macros have major maintainability issues in a multi-person codebase.
Both these things are major disadvantages for automatic comprehensibility of code. Autocompletion can be more-or-less usable but will never be as good as in Java or Scala. Automated refactoring is inherently unsafe in the presence of macros (Scala's fancier typed constructs (typeclasses, for/yield with custom types) mean you need macros much less often; Java tends to force you to expand these things out by hand (or else use annotations which act as de facto macros), which has its own maintainability issues but does at least mean automated refactoring will work correctly).
Some of the language culture pushes people towards less principled abstractions. From this side of the fence that looks like anti-intellectualism; no doubt from their side it's pretension on typed programmers' part. But either way I think they're setting themselves up for long-term maintainability issues (e.g. the semantics of clojure transducers in the presence of errors are infuriatingly not-quite-right, which will either remain a painful gotcha forever, or necessitate a painful migration in the future).
As a minority language Clojure may not be as well supported in the surrounding ecosystem - partly things like IDEs but also code coverage tools, profilers, monitoring.... Remember the JVM ecosystem is wider than just the languages themselves.
There are good things about Clojure, but it's by no means clear-cut.