The real problem with Java in Linux distros
Java is not a first-class citizen in Linux distributions. We generally have decent coverage for Java libraries, but lots of Java software is not packaged at all, or packaged in alternate repositories. Some consider that it's because Linux distribution developers dislike Java and prefer other languages, like C or Python. The reality is slightly different.
Java is fine
There is nothing sufficiently wrong with Java that would cause it to uniformly be a second-class citizen on every distro. It is a widely-used language, especially in the corporate world. It has a vibrant open source community. On servers, it generated very interesting stable (Tomcat) and cutting-edge (Hadoop, Cassandra...) projects. So what grudge do the distributions hold against Java ?
The problem is that Java open source upstream projects do not really release code. Their main artifact is a complete binary distribution, a bundle including their compiled code and a set of third-party libraries they rely on. If you take the Java project point of view, it makes sense: you pick versions of libraries that work for you, test that precise combination, and release the same bundle for all platforms. It makes it easy to use everywhere, especially on operating systems that don't enjoy the greatness of an unified package management system.
That doesn't play well with how Linux distributions package software. We want to avoid code duplication (so that a security update in a library package benefits all software that uses it), so we package libraries separately. We keep those up to date, to benefit from bugfixes and new features. We consider libraries to be part of the platform provided by the Linux distribution.
The Java upstream project consider libraries to be part of the software bundle they release. So they keep the libraries at a precise version they tested, and only update them when they really need to. Essentially, they maintain their own platform of libraries. They do, at their scale, the same work the Linux distributions do. And that's where the real problem lies.
Force software to use your libraries
For simple Java software, stripping the upstream distribution and forcing it to use your platform libraries can work. But that creates friction with upstream projects (since you introduce an untested difference). And that doesn't work with more complex software: swapping libraries below it will just make it fail.
Package all versions of libraries
The next obvious solution is to make separate packages for every version of library that the software uses. The problem is that there is no real convergence on "commonly-used" versions of libraries. There is no ABI protection, nor general guidelines on versioning. You end up having to package each and every minor version of a library that the software happens to want. That doesn't scale well: it creates an explosion in the number of packages, code duplication, security update nightmares, etc. Furthermore, sometimes the Java project patches the libraries they ship with to include a specific feature they need, so it doesn't even match with a real library version anymore.
Note: The distribution that is the closest to implementing this approach is Gentoo, through the SLOT system that lets you have several versions of the same package installed at the same time.
Bundle software with their libraries
At that point, you accept code duplication, so just shipping the precise libraries together with the software doesn't sound that bad of an idea. Unfortunately it's not that simple. Linux distributions must build everything from source code. In most cases, the upstream Java project doesn't ship the source code used in the libraries it bundles. And what about the source code of the build dependencies of your libraries ? In some corner cases, the library project is even abandoned, and its source code lost...
What can we do to fix it ?
So you could say that the biggest issue the Linux distributions have with Java is not really about the language itself. It's about an ecosystem that glorifies binary bundles and not source code. And there is no easy solution around it, that's why you can often hear Java packagers in Linux distributions explain how much they hate Java. That's why there is only a minimal number of Java projects packaged in distributions. Shall we abandon all hope ?
The utopia solution is to aim for a reference platform, reasonably up-to-date libraries that are known to work well together, and encourage all Java upstream developers to use that. That was one of JPackage's goals, but it requires a lot more momentum to succeed. It's very difficult, especially since Java developers often use Windows or OSX.
Another plan is to build a parallel distribution mechanism for Java libraries inside your distro. A Java library wouldn't be shipped as a package anymore. But I think unified package systems are the glory of Linux distributions, so I don't really like that option.
Other issues, for reference
There are a few other issues I didn't mention in this article, to concentrate on the "distributing distributions" aspect. The tarball distributions don't play nice with the FHS, forcing you to play with symlinks to try to keep both worlds happy (and generally making both unhappy). Maven encourages projects to pick precise versions of libraries and stick to them, often resulting in multiple different versions of the same library being used in a given project. Java code tends to build-depend on hundreds of obscure libraries, transforming seemingly-simple packaging work into a man-year exponential effort. Finally, the same dependency inflation issue makes it a non-trivial engagement to contractually support all the dependencies (and build dependencies) of a given software (like Canonical does for software in the Ubuntu main repository).