Some kind of compromise between very specific profeciencies (eg. "Rule Manor" as a proficiency) and very broad/flexible proficiencies (eg. "Persuasion) might be possible. It is very hard to map "Rule Manor" as a proficiency to a skill or capabiity in the fiction... So perhaps some groups might be a better idea. One skill to cover Ruling/Contesting/Creating each holding type, a "Warfare" skill to cover all the war actions, etc.
Something that is a little easier to imagine what it means, rather than "Contest Trade Holding" as a skill.
The stacking rules are cool, they make sense.
The idea of there being Heroic and NPC classes is very much ingrained in D&D. It makes no sense in realworld terms, but in terms of the narrative it kinda does - you have you ordinary dudes and your protagonists/antagonists. Hell, it goes back to 1st edition (I think) with 0th level characters who could never advance beyond that. Removing it changes the flavor, dunno if that is desireable.
I really like that there is a mechanical incentive to go "deep" in a class. Taking 4 levels of fighter actually makes sense mechanically, not only for narrative reasons. Having more flexibility in your bonus actions and more regency is worth it.
After the 4th level, unless you are a caster, you might as well pick up another class. More fighter levels at that point literally have no effect... Perhaps not so awesome. But still, we now have a reason to take more than 1 level of fighter, which is progress.
Could we change the naming scheme a bit? "Experience Elements" is really clunky. The system seems solid, but eg. "Tier", "Level" and "Experience" would make more sense to me than "Level", "Experience" and "Experience Element". Especially if one is coming from D&D 3.x.
I'm curious RP - how does the domain caster rules detract from the focus? What they change is primary the dependence of caster domains on their regent... or is it that any domain can pick up a bit of casting by grabbing a few temple holdings? You still really need a highlevel holding to gain a substantial caster level and I assume spell level is still limited by highest holding level.
Regency collection for a 9th level char might be a little out of hand... province + 4½ holding types... wow. Then again, that's largely academic, since I assume the only Paramount character is the Gorgon or equivalent.
The bit about upgrading generic classes seems kinda superfluous... how often is a character going to switch from commoner to *whatever*? THe only place I see them coming into play... and they are kinda confusing. Saying "commoners use generic classes, the others use specific classes"or some such might be simpler. I might be misreading the rules though.