In Java, developers will bundle dozens of random .jar files with their application. Other versions of these libraries may exist in a Linux distribution already, but specific Java apps aren't linking to those and carefully documenting how to install all the dependencies (or which ones are optional). Instead, from the distro's point of view, these Java apps are being released with a bunch of binary blobs that may or may not contain bugs that need patching later. Which partly defeats the purpose of package management.
Python programmers don't do this. Distros love Python, which is why so many of their system administration/automation scripts depend on it. This puts some tension between packagers, who use it as a bash/perl replacement, and developers like Zed, who want to treat it like an up-to-date library -- but realize that the Java solution of just bundling the whole thing with the main app is ugly. That tension exists because Python developers haven't run amok the way Java developers have.
BTW this rant about impossibility to upgrade is a classic one and nonetheless wrong. You're perfectly able to install new versions of python, or perl or whatever given that you do that in /usr/local to keep the official version alongside the new one. I do this all the time, my system comes with perl 5.10 but I regularly install the newest releases in /usr/local, or even development versions. No problem.
As long as you know about it, you can fix scripts, but any downloaded program needs a change in shbang line, or at least running explicitly via python-2.X.
But yes, "most Linux distros" part is completely untrue. Most have at least 2.5 - or higher.
Seriously, unless you're working in C/++, I think it's only worth using the system-bundled languages if you're actually targeting the OS itself. If you're targeting more than one platform, using your own build seems to be the only way to stay sane. If you're only targeting a single platform, unless you're tracking a bleeding-edge-style distro like Arch, you can guarantee that all the fun development is going to be going on somewhere you can't reach.
Luckily, we have checkinstall.