How much authority does the Emperor/Elder Council have over the provinces?

In the games Daggerfall and Skyrim, the respective provinces of High Rock and Skyrim seem to be largely independant and apparently conserve their traditional native political institutions. In Skyrim we see that in each Hold there is a representative of the imperial military, but I get the feeling that this presence is due to the civil war.

I would like to contrast these provinces (High Rock and Skyrim) with Morrowind in the late third era: In Morrowind the imperial presence is quite evident, with there being an Imperial-assigned Duke presiding over each District (assuming Vvardenfell is not the only district with a Duchy), each with their District Council, presumaby made up of representatives of the Great Houses. Oh, and let's not forget the King of Morrowind.
I find it strange that there is so much more imperial authority in Morrowind when supposedly the Treaty of the Armistice granted exceptional political and religious autonomy to Morrowind.

Why don't the Great Houses have the same authority as the kings of High Rock and Skyrim?
What is the equivalent of the Dukes of Morrowind in High Rock and Skyrim, if any?
In the time before the civil war in Skyrim, was there an imperial governor acting out of Castle Dour?

It's all for show in Skyrim. The High King is pretty much a puppet of the Empire, as noted by Stormcloak supporters and http://www.imperial-library.info/content/skyrims-rule. Skyrim is (historically) more supportive of the Empire than Morrowind, so they usually just need to act via the High King (though this is speculation).

The Dukes of Morrowind existed before the Empire was there, from what I can tell pretty much in the same structure with the same rights and what not. King Hlaalu Helseth is an imperial king that is certain but his power does not seem to reach much further then Mournhold and in that sense he's not much more powerful then the Duke of Mournhold would have been before the Empire. Morrowind also had her own laws, could make her own laws and had three god kings that pretty much ruled over whatever happened. The Empire had certain rights, like stationing troops, seeing that mutually agreed upon laws were upheld and the rights to mine for Ebony but besides that it was the houses that made up the mayor force of power in Morrowind.

In Skyrim it seems far more like the Empire making the laws and the Jarls making sure the laws are upheld. This is possible in a largely friendly nation, in Morrowind the presence of the legion would be required to make sure that people follow the law. In Skyrim it would be redundant, you would already have a culture that's largely follows the same laws and traditions and any army stationed there would exist primarily out of Nord soldiers. Also you have to remember that in the 200 years since the Septim line ended a lot of changes would likely have happened, especially after the great war.

What we see in Cyrodiil is local law pretty much doing what the legion should have done, where most of the legion is outside of the Imperial province and instead based in other provinces where they are actually needed.

I have no real excuse for the situation in High Rock, but maybe the same applies as in Skyrim.