First ignoring the complexity of the dependencies between every module and how complex it may be to maintain for the Bioperl devs...
I can't ignore that - it's the biggest problem! Dividing up the modules along functional lines is probably a win for users that just need a little piece but it will definitely cause problems for the developers.
If the developers are willing, sure, there's no reason they couldn't create 20 distributions instead of one, with a spider's web of dependencies carefully setup to link them together as needed. They could also just start mailing you free beer when you get thirsty! Might as well ask for that while you're at it.
-sam