Well yes that is a downside, but instead of having full control you could be able to give input like if you are a LB coach you could say, 'give me coverage linebackers', you could still have a lot of these features such as pushing for certain players and depending upon your influence on the team your opinion might be taken under consideration.
Also another thing that would be cool is to have a mentor, for example you are a Eagle DL coach and through the year you gain knowledge of Jim Johnson's system gradually and get to the point that you have the ability to take that system wherever you go and be able to implement it successfully.