/etc/init.d/tomcat-6, line 23 should include "-d" so that dependant JARs get added automagically to the classpath.
Adding -d has it's downside too, it usually pulls in a lot more than you want often with no ill effect. However, if things go wrong, for example a "can't find class error" is a lot easier to read, debug and solve than some other vendor specific error gibberish due to using different versions of the same library at the same time resulting in symbol collisions and other funny stuff.
Adding -d has also the effect that updating or reconfiguring a system installed package somewhere down the dependency chain may change the classpath of your server drastically making things rather complex to predict. And that by default?
There is also the aspect of someone wanting as few jars as possible on the global / common classpath. Adding is easier than removing.
Last but not least it's perfectly fine to run java-config in the corresponding /etc/conf.d/tomcat-6 to construct a TOMCAT_EXTRA_CLASSPATH.
To sum up, a meager "should include -d' isn't convincing enough.
If at all we go into the opposite direction. See bug 453212