Many kinds; Java itself, and lack of stable dynamic redeploying without bringing the services down, despite being marketed otherwise. I'm talking about real life production configurations, not about what's possible on Joe R. Hacker's machine under special circumstances. Of course it's not the fault of appservers themselves but rather of JVM architecture esp. classloaders. Still the RL situation is that today's complicated stacks of libraries, dependency injection frameworks and code using it can make life of admins and change management folks miserable.
Add to it a monstrosity from the deepest ends of Moria: maven (hint: google for 'maven sucks') and you have the world lots of people want to forget about.
Today's Clojure webservers being usually wrappers around existing solutions won't cure all these wounds, but at least it's a step in a refreshing direction.
You could say nothing, technically, but that wouldn't reflect real life situations and existing "best" practices.
It's usually used to build deployments, CI, autodeploying and stuff. In fact for many operations tasks Maven cannot be decoupled, because it's used for almost everything. When using Makefile, to copy a compiled archive to a destination you'd use shell commands; in Maven you cannot leave the Java world so you pick up a plugin to do the same, usually of poor quality. This way you introduce even more code, which is hardly manageable at some point, and contrary to the maxim "every line of code not written is a correct one".
Short answer:
Pick a job in operations or change management at a large Java shop, then you'll know.
This still has nothing to do with using a Java app server. You could be using other tools to handle those tasks just as easily. Even if you have developers that love Maven and use it to build and package their applications, this certainly doesn't mean you need to use the tool for other tasks in which you find it to be a poor fit.
I wish you having this freedom you're talking about on all your projects.
The RL is that in most shops usage of appserver & Maven is tighly coupled to the high ends of pain, and you don't decide the next big thing that could replace even parts of this sick marriage. Of course maybe you're talking about a situation when you decide about the whole infrastructure but then there are big chances you wouldn't choose Java in the first place. So please make a distinction if you're talking about theoretical "who could do what" or practical "what's already going on this planet" or even more practical "I'm gonna conquer the world with the new X and I really have freedom to choose it" :]
Add to it a monstrosity from the deepest ends of Moria: maven (hint: google for 'maven sucks') and you have the world lots of people want to forget about.
Today's Clojure webservers being usually wrappers around existing solutions won't cure all these wounds, but at least it's a step in a refreshing direction.