I just ran into this same issue. It's really painful having the Loggers named by the class name only without the package name because it makes it nearly impossible to control the logging level. As above, Log4j (and most other) logging systems are designed to be hierachical making it easy to turn on/off logging at the package level. I'm using v2.0.5, is there a plan to fix this anytime soon. Do you accept patches? I would point out that if you're using obfuscation for some reason but keep the Loggers named with their actual class name you've mostly defeated the obfuscation anyhow so I'm not sure why you don't just go back to using class.getName()?
Thanks,
Corey