Use drush make to load only modules?
If you run drush make --contrib-destination=sites/mysite, then modules will be placed in sites/mysite/modules.  rsync is going to be faster than Drush make. (Edit: This speed comparison presumes roughly equal transfer speeds between the endpoints. I can see how make might be faster if you have a fast connection from the target to d.o, but a slow connection between the source and the target.)

If you want to create a makefile for an existing site, you may use drush generate-makefile, or build a whole installation profile with drush generate-profile.