I want to do a lot of filtering of input and output and I need my stuff to be in handlers in the first place.

I don't think that is necesary anymore. The filtering stuff is much more powerful in mod_perl2 (mainly because of the underlying changes to Apache2).

In mod_perl1 you could only filter responses generated in mod_perl with a mod_perl filter (using Apache::Filter or one of the other chaining modules).

In mod_perl2, you can write a filter in perl that can parse the output of any other apache module. In fact, mod_include is now also written specifically as a filter. So as an example, you could have a Java servlet whose output is filtered though mod_include, and then filtered again through a mod_perl2 filter.

See the mod_perl2 Filter docs for more info.