Fun note: I believe that's the book series Jim Butcher wrote on a dare. Jim Butcher challenged someone on an internet forum to give him the two worst ideas you could possibly turn into a book, and he'd turn them into a best seller. They gave him Pokemon and the lost Romain legion.
It looks like you're looking at new classes, yeah, or you could just add "Furies" on top of the normal class. I'm not very familiar with Eberron's dragon marks, but it sounds like importing and tweaking a mechanic like that might work for you.
havent read these books. but i had an idea where as a player would level, its powers in a secondary chart (unknown to the players) would grow. little things they would notice changing, and learn in the end to control.
My idea was, as they leveled they each became more like an elemental of a type that suited their class choice.
For example, a fighter/barbarian would take earth. Would gain strength and constitution, the ability to move earth etc as the levels grew.
Id say soemthing like that, but suited to your idea of the info. that way if it levels with the players it wont be heaps op at low levels. and at high levels just bump the CR of encounters up.
I know the series you mean, and thinking about it, I'd suggest using the Summoner class from the APG, perhaps making some custom archetypes for the different Furies.
Commoners might only have a dip in Summoner, giving them a weak Fury and then other class abilities. Nobles might have more levels, or take the broodmaster archetype for variety etc.