Holmgren is a west-coast offense pass-happy coach. He spent his formative years with BYU and the 49er's under Bill Walsh. He wants an offense where the focus is on the passing game. In his system, the running game should mainly exist to support the passing game.
Shaun is a great runner, but isn't as good as some other backs in the role of receiver. He's decent, but Holmgren has questioned his willingness to work at being a better all-around back. Shaun wants to run the ball... that's his strong suit... and Holmgren wants something else from Shaun, that might not be a strength.
When at Alabama, Shaun was criticized sometimes for not making an effort to improve his pass-blocking skills. That was supposedly why he wasn't made a starter until his junior year. I remember the statement being made by one of Stallings coaches that Shaun wasn't keen on practicing and learning all of the roles that a running back must fulfill. He was acknowledged as the best pure running back even as a freshman, but until he made strides across the board in all phases, he wouldn't start.
I know that Shaun likes Seattle and would like to stay there but, even as well as he has done there, I think that he might be a better fit somewhere else. If he was implemented into a system that really fit his strong suit, he would probably be the unquestioned premier back in the league.