There are things I'd love to see added to the Stripe Billing APIs (some of which I mentioned in the article), but I have a really healthy respect for the amount of good work that's gone into the design of an API that, as you say, touches just about every part of a potential customer/payments workflow.
Stripe's API has consistent naming, a clean design of the core data objects, consistent data formatting and request patterns, good dashboard tools for seeing what's happened in requests and webhooks, and great documentation. All of which are non-trivial, and basically none of which any of the other "name brand" APIs I've used in the last year or so do. :-)