Pol was at Honda for two seasons and in both seasons, he finished behind Marc, even with Marc missing time through injury.
Throughout his time with them, Marc was the focal point in their development which is the reason why nobody but him could actually do something with that bike, until not even Marc could ride it anymore.
Marc himself openly admitted to guiding development away from his teammates if they were starting to get comfortable on the bike.
When Dani Pedrosa left Honda, he wanted to continue as a test rider, but Honda turned him away because he was too small...
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If you read the above article, Marc spoke glowingly of Pedrosa as a development rider, but ironically in his own admission ''sabotage'' him as his teammate. And then when Honda rejected Pedrosa as a development rider because he wasn't like Marc, they started losing their direction.
Honda put everything into Marc, building that bike around him and expecting him to always be there. When that bike chewed him up and spat him out, they were screwed.