This is not due to the upgrade to jython 2.5.3 but to an incorrect library used, that is jython instead of jython-standalone.
It seems that the move to a gradle based build system is causing some trouble. Fortunately, it has been fixed already by https://android-review.googlesource.com/#/c/59173/1 which is now merged, so by the time Android SDK Tools Rev. 22.0.1 is out the problem would be in the rear-view mirror.
In the meantime, you can apply this simple workaround:
- Download jython-standalone-2.5.3.jar
/tools/lib/jython-2.5.3.jaras jython-2.5.3.jar.ORI (just in case you need it)
- Symlink (or copy, if your OS does not support symlinks ;-) jython-standalone-2.5.3.jar to jython-2.5.3.jar