The second is startup speed, which doesn't sound like a bit problem when you're doing a mod_perl app, unless you're heavy into unit tests, in which case the startup hit for pulling in several tens or hundreds of modules bites you every time you execute a .t file. And when you have several hundred tests (a good thing), the additional startup can add minutes to a full test run (a bad thing).
This problem can (as I'm sure you know :-) be mitigated by building and tearing down your own test fixtures in a single test script rather that using lots of different *.t scripts to isolate your tests.
I'd probably look towards optimising the test suite before I add the extra overhead of rewriting / inlining modules.