Well, I'd argue that the protocol hasn't been designed correctly. Don't forget that every single website out there use HTTP as their main protocol, yet, they have very different feature sets, capabilities and even goals!
Wasn't this what CORBA, XML-RPC, or SOAP was meant to solve? And then we all happily ditched them for loosely defined RESTy JSON because it was so goddamn easier.
I think TFA is describing a legitimate complaint; but I don't think the RESTy CRUD twitter exposes is all that difficult to abstract.
Amazon on the other hand…
There are some problems with no good solution, namely the signed parameters in Amazon's case. How do you sign JSON? Is there a "canonical" JSON format that will allow signing consistently, and verification? All the approaches I've seen are incompatible in some way.
Client-side SSL is another solution, but its much less flexible (i.e., token-generated requests wouldn't be easy)