Is it acceptable for a President to micro-manage?
For example: Suppose an agency or department is engaged in some regulatory action of questionable interpretation. It has come to your attention as President and you think the agency/department in question should back off. Do you contact the head and tell them to back off? Or, do you stay back and either let it go or let your disapproval filter down through some other way?
I tend to think it's ok, as long as its kept discreet and is not over-done. I'm sure there could be accusations of favoritism, but to me it's no different than a pardon. You could consider this a pre-emptive pardon, if you will.
Please note that "questionable interpretation" is key here. We all know that government bureaucrats are not immune from making stuff up as they go.