A sensible system seems like it would be three tiered:
Very small stuff would remain unregulated - obviously there is no concern with things like the CX-10, right? I can't imagine a "drone" of anything near that size causing any size of full-scale aircraft problems.
Mid-tier stuff would be a world like Amateur Radio - modernized to be online or something as you've suggested. You are free to participate in the big boy's airspace within the rules, but some education and proof-of-knowledge about those rules is required.
... and of course large things should not be any different than a full-sized aircraft, with the same regulations.