I don't see how introducing him with Phil Coulson supposedly undercuts him. And you keep referencing his lack of use, but he's been pretty consistently appearing in the books since his introduction. Maybe not the most mainstream titles, but since his introduction he's been in two volumes of Secret Avengers as a lead, was a main character in Paul Cornell's Wolverine mini, had his own fantastic mini series by Robinson, another fantastic mini by Declan Slavey in CW2 and some recent appearances in Punisher. I'm sure they're more I'm not thinking of. And each of these appearance he's there are an agent of SHIELD. Competent but young, dealing with the legacy of his name and what that entails. It's not like sometimes he shows up and he's the director, other times they have him in the field. He's been pretty consistent so I don't understand the mixed messaging.
If the reasoning is he clearly is there because for synergy purposes then ok? It's not like its one or the other. You can have a character in your books that looks like the character in the movies while still deciding you want your book character to fill a different role. The two are not mutually exclusive. Unless I've missed something I don't see the mixed messaging.