The only thing that an "experienced" marshal has over a newbie marshal is the Leadership skill. If you train Leadership at the academy, you could easily have full access to all marshal settings for the instant you are appointed as marshal. Which is really the whole point of academy training. So there's no reason to toss the whole idea out the window.
What you can do is tie the implementation of these formations into the leadership skill rating.
* Higher leadership: + chance of success
* Very high leadership: ++ chance of success
* Specifying more options = - chance of success
* Specifying "overrides" for noble units settings (formation, encounter reactions, etc.) = -- chance of failure
Put all this together and calculate a chance to successfully implement a formation. If you fail, the consequences could range from nobles just lining up according to their personal settings, to being +/1 a line, depending on how badly you failed.
For an Epic Fail, when a newbie marshal tries to use a super-complex setting with lots of overrides, you could even assign completely random lines to each individual noble on that side.
And you can even tie in the number of available custom formations to the leadership skill. One custom formation stored per 20% skill?