What PC class should a well-designed ruler have?

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So here are a few options that might work for you:

First off I think Paladin of Freedom might be a better option here than fighter. He starts with bluff and sense motives, he is a charismatic fighter and he would have the thematic drive to usurp the old ruler. Also you could add in Harmonious Knight ACLs and From Smite to Song feat to have more of a leader type of feel.

Harmonious Knight Paladin of Freedom 6/Feat Rogue 2 actually looks like quite a good fit for your leader all around and if he gains a level or two you could look at legendary leader or warmaster for finish things off.

On the sidenote of the issues with Noble class, you are the DM so you could simply say he qualifies for Noble once he becomes the lord and at which point he starts to undergo training as a noble. That seems pretty reasonable to me and doesn't fall to far outside the requirements for the class.