1. Capital Requirements, licensing and Bonding for people who hold money for consumers who are not banks. These rules are consumer protection laws and make sense for businesses that offer custodial accounts denominated in bitcoin or dollars. These rules could have been applied to Instawallet, Coinbase, Mt. Gox, etc.
2. AML + KYC rules. These require people who help move money into and out of the banking system to find out who their customers are and report them to law enforcement when they do the unexpected. These rules could be applied normally to people doing exchange services, like Expresscoin, BitInstant (RIP), CoInvoice, etc.
I've spent years and hundreds of thousands of investor dollars examining the issues here, like you have. Stay tuned for a policy piece describing when these rules make sense and when they don't. Hint: If you are just posting software to github, these rules do not make sense to apply to you.