You must realize that skaven are not very magicaly adept.
Only Grey Seers (which are very, very rare) can perform magic, and even then they need to consume refined warpstone to help them.
This does not mean skaven magic is weak, on the contrary the raw warping choas of their magics is highly dangerous to all involved.
edit: Considder this: What skaven lack in intelligence they make up in cunning, their magic is like that too. Not elegant and fully thought out, but insidious and it is likely to come back to bite your tail off.
Of all the clans,
Pestillence is the most independent civilization.
They have their own interpretation of religion, their own bubonic magics, independent Grey seers (act as priests) and such. The magics that fever-addled priests have scratched down during their long exile in Lustria have much in common with those used by those subverted by the Nurgle.
Skryre are mostly about warp lightning and subversion of alien(bright etc)magics to work for chaos. They use mechanical means to visualize and manipulate the winds of magic, most often employing warpstone, runes and other esotheric apparatus.
Moulder are more like bio-engeneering alchemists using warpstone.
Eshin possibly has it's own magics, assisting stealth, but those are shrouded in secrets. They are known to use warpstone somehow to create esotheric toxic weapons.
Mainstream Warlord Clans get their magic in the form of echanted weapons, created by either the mystic GreySeers or more commonly by clan Skryre. Again commonly using warpstone to magnify the malignancy of the spells and runes forged into the item.
Grey Seers are the most intelligent and cunning of all skaven, they enjoy the favour of the Horned One (as long as they are succesfull in their intrigues). Infighting in Skaven society is harch and machiavellian, as such the un-naturally long-lived Seers inevitably rise to the upper ranks. Which is to say the grey Counsil.
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I'm not quite sure how clans might work and interact as seperate civs.
It is a wholly different concept from the clan influence by religion-mechanics.
I assume the Skryre, warlord clan, and grey seers are available to all.
Will all skaven civs have access to eachother's special units? (but at a double cost.) Maybe award money to the relevant clan if a special unit is built by another skaven civ?
How will the Grey Counsil be worked out?
Assume the player is one of the members.
Is the grey counsil a vassal system? (ie will skaven have high tendency to ally eachother?...skaven DO fight easilly, maybe also let them forget grudges easilly. They are cowardly back-stabbers after all.)
How to manipulate the counsil? -auction in warptokens? (buy influence)
Might be something like the UN.
with resolutions, weighted votes etc. "all declare war on known civ X".
I think I'm off-topic now.
sorry.