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?
I think you're going about this the wrong way. I think that the options within the Formation Builder should have the Leadership requirements. The way you had it sounds reliant on D&D style dice rolls. Here is what I propose:
Leadership and/or H/P unlocks the Formation Builder. Because the Marshal does not always have experience in telling nobles how to precisely deploy their unit (outside of formations), an additional Leadership value will be required (to formulate a new strategy) for each level of sophistication.
Basic formation options such as Infantry, Cav, and Archers being deployed in the Front, Middle, Back, and Rearguard be made available immediately in the Formation Builder, but only in baby steps. Defaulting to what is possible with Infantry Charge, Archer Opening, Fortification Deploy, and Infantry Wall. As leadership improves, or maybe even use of custom formations increases by the Marshal, more options such as having the infantry deploy in Rearguard, and Cav deploy in the front, become available.
Eventually, when the Marshal is able to use some of the very advanced stuff, such as Weakening Skirmish, they will still not be able to change Withdraw settings in the Formation Builder. They will still need to increase their Leadership (or use more custom formations).
Perhaps also limit to how many formations they are able to have or use through the Formation Builder? If someone had 10 custom formations, then ya, units would become travel bots. But if they could only have say, one attack formation and one defence formation, then not really.
What I would like to see though, is be able to have maybe ten custom formations available, but only have one or two "active" to use within a given time frame. Example:
I have Formations named: Slay Those Monsters, Skeleton Explosion, Eat His Horses, and Bite the Dust. I choose to have Slay Those Monsters and Eat His Horses active. I decide that since the other guy doesn't tend to have a lot of cavalry, that I want to be able to use Bite the Dust instead. Well, now I have to wait a week, two weeks, or something in order to actually be able to use it. In the mean time, I still have to issue new line settings to nobles in my army so that I can hopefully mimic that formation.
And since people WILL forget what each setting does, a way to review what is in each formation the marshal has created.
