I find it amusing how you get the right idea, to divide Skaven into their Clan subfactions but then you go on and say "there is this one elven race with 3 subfactions (High, Dark, Wood)". To be precise, if we do them the same justice as you want for Skaven, it is more like
Back to Skaven, we have the for Great Clans
Clan Skryre, technological savants
Clan Eshin, stealthy assassins
Clan Moulder, breeders of fighting beasts
Clan Pestilens, spreaders of disease and plague
and several "normal" Clans building the bulk of the armies. In my opinion including Clan Mors would be a solid option to represent them. It would also offer the (DLC) option to include Queek Headtaker for some Karak Eight Peaks action.
At the moment, it looks like Karl Franz has to unite 11 lords for his empire. There is not much imagination needed to assume that Grimgor Ironhide also will have to conquer several greenskin tribes on his way (a forest goblin tribe for spider access as example). And if two can play that game it should be logical that the five different Vampire Bloodlines and several Dwarf Clans could be used in the same way to focus on some civil war besides conquering the Old World. And that such a powerplay would also be used for expansion races, since every armybook can field some subfactions. So I do not doubt we will see some Skaven subfactions.
The real elephant in the room is still: If we do not play the story driven campaign with a "preset" leader (like a skirmish game or multiplayer), is there an option to choose a leader and faction for personal preferences? Could I lead Clan Eshin to victory or conquer the world with Crooked Moon Nightgoblins?
Or is something like this the first big mod to come
-----Red Dox