It all depends on wether you make a totally new Tech Tree or not. The Game is balanced in Vanilla (somehow), so tinkering with that makes balance go awry. For example, if you add a Unit to the Middle Ages, it can upsed the gameplay if it's better than other units, but if it doesn't have a unique role, what's the point? And there's not enough Unit Graphics... You can use some of the unique and scenario units, but it is doubtful that you can fill the whole Tree with "medieval looking" units.
One Idea would be thus to "copy" the vanilla tree. Rename the Ancient Era "Age of Dawn" and so on and just move the techs up instead of adding so many new techs in the Middle Ages that they don't fit on the screen... something like Knights would be in the place of the Lancer now... the Musketman would be where the Infantry is.
Or one could simply fill the Middle Age more that it is now and slow Tech Progress and cap it off at Muskets. Good enough, simpler is always better.
Regarding Wonders, the Big Keeps are a good idea (Eyrie, Red Keep, Casterly Rock, etc. ...) But they somehow tie into the scenario vs. mod problem, because in the scenario, they are actually just the palaces... . Other ideas can be the Isle of Faces, the Dragonpit, the Twins, the big Church, why not a Baelor-Statue/Tower?). As a Building, an Inn is a must. What about the Magic?
Regarding Social Policies, I like the Religions as Policies that cancel each other out. Other Trees can stay, things like Tradition, Rationalism, Commerce, "the City-STate-Tree". It depends a lot on Gameplay here. Each Gameplay style (Tall <-> Wide <-> Conquest and Tile <-> Specialist) needs to be viable and present, and of course, they all need to be connected to Victory Conditions. The United Nations can easily be changed into a "Lord Council" if the city states are lesser Houses. Whoever gets most, gets "elected king". But that is confined to Westeros! So we are now to a full circle wether scenario or Modification. If you go the first, you can specialize way more, otherwise balance must be there, but it's "less detail work". Also: Flavour or Realism: Direwolfs as a Stark-Unit or a promotion for 5 special units of them or nothing? Special Units? Kingsguar
Anyway, take the slow road and publish any beta you can so we can comment and you can build step by step. As you can see above, it's easy to get lost... Very lost. So my advice step by step: For example, do the techs first and add the new units (Huscarl from the Denmark scenario, f.e.).* Then go on to the Wonders and Buildings. Do the Social Policies. Balance the Civs. If you the mod way, you can now adapt it to a specific map.
EDIT: In short: If you want the mod or scenario to be more than just flavour ("Oh cool, I can play as the Lannisters"), you need to have a general idea (not detailled). Otherwise it's a nice mod you play once to see the units and the map, but not more...
but I really mean to ask how are you going to divide the civs?
