I think Honda fails for the exact same reason why Toyota has failed in Formula 1. Maybe it's how the chain of decision making works in Japanese companies based on respect on no room for error.
When McLaren engineer A responsible for the engine opts for an improved part he has to ask the chief engineer B, chief B has to ask permission to the team manager C, who will discuss it with the responsible guy from Honda Motors Mr D, Mr D has to seek permission from Mr E back in the Japan based factory, who then needs approval from the R&D guy above him Mr F. Eventually the CEO of Honda Mr Z will have to sign it off and the decision can water down all the way back to engineer A.
In the meantime the Brits, Germans, French and Italians have developed an entire new engine while Honda is still making decisions about a single part.
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With that said I don't understand how Japanese motorcycle companies are so dominant in two wheel motorsports for the last 40 years, so maybe I am just talking out of my behind here.