The protocol is documented in the client source code, in the wiki, and most of the gaps can be figured out by simply looking at existing transactions and their effects. (Each transaction is published along with precisely what changes it made.) I agree the documentation could be a lot better, but I don't think you'll find people who have questions about the protocol that haven't been answered.

With the vast majority of other payment systems, not only is there no documentation of their internal protocol but even if you knew their internal protocol, you still could neither see nor submit a transaction. With Ripple, anyone can see any transaction and anyone can submit a transaction and if it meets objective criteria, it will be processed.