As the article says, Bernstein's stuff won out because his work is at the intersection of solid crypto, clean and performant code, and sane API design. This, coupled with the NIST curve debacle that shook public confidence, makes for a compelling case.

Part of the problem is there is often a wide gulf between cryptographers and the authors of libraries who then go on to use those algorithms. This is perhaps more acute with approved-by-committee, standardized crypto because library authors may have to implement it to be compatible, despite not being experts in the particular algorithm.

In Bernstein's case, he ships (through NaCl) a reference implementation that is good enough to be used in production, and packages complete constructs in ways that are resistant to misuse. This is his innovation -- other libraries tend to offer only the primitives and rely on the user to chain them together in ways that make sense and never in the ways that don't.

There are other cryptographers that ship decent reference implementations -- the Keccak team being one -- but their work is largely restricted to sponges and any construct that can be formed out of it (e.g. PRFs, stream ciphers, hash functions). There is perhaps a shortage of people who look at holistic cryptosystems and possess both the domain knowledge and the ideal attitude towards misuse-resistant design.