Drivetrain: If you go for an internal-shifting hub, no big deal. Just a rear wheel rebuild and running cable to the handlebars. If you go freewheel, you'll have to get a rear der. hanger added, which means a new dropout on the drive side -- plus you'll have to rebuild the wheel to get a freewheel or freehub hub in there.
Then you've got brakes to deal with. That's going to be a pain in the ass, likely requiring the frame to be welded/brazed. If you don't have posts for caliper/v-brakes, then you'll have to get cantilever brakes, most of which are road and won't clear cruiser tires. Cantilevers still require a hole in the fork and a brake bridge + hole in the rear. You'll also want to make sure the frame and fork can handle braking forces from the new brakes. It's likely that they'll be fine, but they're not structurally required to deal with those forces, and you could fold a fork or fold your seat stays.
Internal shifting hubs often come with drum brakes, which work just like your default cruiser setup:
http://www.xxcycle.com/php/boutique/...1&FROM=froogle
I think you should go for the internal shifting hub solution.