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Well I'm not exactly sure what the defining characteristics of the "best" is and if it is different than CK2, but some notable discoveries I have made:
Bohemia is an EIGHT county Duchy. Additionally three of these counties have 6 development slots.

The Duchy of Transylvania has 7 counties.

For individual counties, Rashka and Guranj are the only 7-slot counties that I've been able to locate.

I imagine the new Special Buildings might also come into play and I'm not at all familiar with what all of them are or what each one does.
 
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It gets more complicated yet as terrain bonuses add or remove additional value from counties.

As an example, the farmland terrain bonus will accelerate development in the counties where it is present compared with other, slower developing terrain types.
 
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Yup it's much more complicated. The county and barony counts do matter, but terrain is also very important, so it may shuffle things quite a lot too.
 
If it is only the ratio of counties to possible holdings (cph, lower=better), best are these:
Ötüken - 0,1765 cph
Uzboy - 0,1818 cph
Rashka - 0,1905 cph
Ferghana - 0,1923 cph

Data from: https://ck3.paradoxwikis.com/Duchies

Of course now one has to take development potential, great holdings etc. into account.

England seems quite strong:
york with 0,21 cph is quie good, water access combined with essex (0,26 cph) and London, a special project possibility, is 9 counties together which might be possible to achieve as demense limit. Alternatively, east anglia next do both wait for you, with 7, respectively 8 combined counties.

Valois is also quite strong, 0,27 cph, and a superb special project (notre dam). It is 7 counties on its own, so might not be easily combineable with an additional duchy.
 
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From what I have seen so far, there is one capital location that seems much stronger than all the others: Baghdad.

It has 6 holding slots, all of which are floodplains, and the house of wisdom as a special building.
 
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I'm pretty sure it's Thrace. You have one six-barony county, one five-barony country, and Constantinople. The Theodosian walls alone are almost certainly better than a seven-barony county: you have quadruple your normal capital levies and money, which I really doubt six barons can beat. Then there's a duchy-wide buff the walls grant.

But IN ADDITION, you get the Hagia Sophia. Where do I even begin. Learning, Intrigue, Piety that scales with your Knights,, 20% Knight Effectiveness(!), +2 Knights! It's crazy!

The other big thing is that you can hold Thrace and probably another super good Duchy (or flexibly hold counties to do things with), because it's just 3 counties. But even if things go wrong -- if you have a bad Gravelkind or something -- you always hold Constantinople. And Constantinople is AMAZING.
 
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If it is only the ratio of counties to possible holdings (cph, lower=better), best are these:
Ötüken - 0,1765 cph
Uzboy - 0,1818 cph
Rashka - 0,1905 cph
Ferghana - 0,1923 cph

Data from: https://ck3.paradoxwikis.com/Duchies

Of course now one has to take development potential, great holdings etc. into account.

England seems quite strong:
york with 0,21 cph is quie good, water access combined with essex (0,26 cph) and London, a special project possibility, is 9 counties together which might be possible to achieve as demense limit. Alternatively, east anglia next do both wait for you, with 7, respectively 8 combined counties.

Valois is also quite strong, 0,27 cph, and a superb special project (notre dam). It is 7 counties on its own, so might not be easily combineable with an additional duchy.


To bad that they Made Rashka the worst start in the whole game, ahistorical diversity broke one of the most interesting nations and region in all of EU4 and CK historically and gameplaywise. It's completely broken.
 
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To bad that they Made Rashka the worst start in the whole game, ahistorical diversity broke one of the most interesting nations and region in all of EU4 and CK historically and gameplaywise. It's completely broken.

See I kind of like that. It's super hard but you get to start in a really good duchy. There are lots of awesome duchies you can start in but the game is too easy.
 
Now, addressing the title.

Probably the 2 best duchys to hold and control are Trace and Palestine, with all of their counties (at least in general and playing abrahamic)