I have mixed feelings about the faction system as mentioned above. On one hand I think it is fantastic to add something new to the continuous grind. It certainly makes sense to build up an affinity with a given element. Losing affinity with the diametrically opposed element also makes sense. Were I less prone to switching and playing with different decks at any given moment I would be completely in love with it. I guess life is about choices.
Another possibility is after reaching certain heights in loyalty to 1 faction, you might start to lose loyalty in all the others especially those close to diametrically opposed faction. "If Wizardbob is that loyal to faction x, it calls into question his supposed loyalty to us." This would make sure that no one is ranked highly in more than 1 faction.
It almost seems like this could utilize some of the Arena concepts. Each empire could have the different level of outposts corresponding to the levels of the arena. If you attack the remote remote outpost it would be the bronze level people of that faction. While assaulting the castle would be platinum level loyalists.
I was actually planning on writing up some sort of proposal for this, but having stumbled upon this is much better! Trying to sell an idea to someone else who would have to do all the work is so much harder.
As to the card creation, I think that is an excellent idea. I think perhaps might first have to win a blueprint/recipe/summoning spell etc through questing. Perhaps different level blue prints. The very best of course only available through the highest level of conquest. (Have fun storming the castle!) Not every succesful raid would garner blueprint. Materials could require raiding as well. Steel/Stone in the empire of Earth, Glass in the empire of Time, Wood in the empire of Wood for instance. For materials in empire that you are attuned with however, maybe have option of Defend the Realm to face AI 'invaders' to win materials in payment. Blue prints also maybe available through events and donations. Perhaps even lucky oracle spins.
Perhaps the pets could be tied to your loyalty. At certain tiers of rank new pets become available. Can either have only 1 pet at a time or perhaps even have a stable where you can park one while you trot out another. In fact, I think it would be great if everyone started with 1 and could only get addional stalls via winning events or through donations.
Clearly I have gone far afield and maybe a tad crazy. The ideas in the original post just created way too much excitement in me that I failed to suppress. I have never been more excited about this game than I was when I read those ideas. If I gone too far down a narrow pass, please forgive me. I simply more ideas than self control.