Interesting idea.
You know how currently you have fortress strength which works like a fortresses health points and that you can raise them using certain cards. Would the kind of cards be constructions like walls and whatnot, or would walls be played like in MtG? I prefer the latter myself.
I had an idea myself that you might find interesting.
You could keep track of two counts, one being Fortress Population(FP) and another being Fortress Morale/Mood(FM). You'd start with 7 FP and can raise it with either migrant cards or birth cards. When drawn migrant cards would be played into the battle so the enemy can attack them for a turn before they get to your fortress and add to your FP then placed back in your deck. You loose FP when you play creature cards that recruit members of the population into the military or when you don't defend against besieging creatures attacks. You can gain FM by playing Legendary Dinning Room, Decorative Waterfall or Well cards which would cost you resources. You loose FM when you loose FP one per FP lost and when Soldiers die, different types of Soldiers would cause you to loose more FM than others so beloved Champions deaths might upset more than simple infantry deaths. A low FM could cause penalties for soldiers on the battlefield, stop/lower migration(?) and if it reached zero then expect your fortress to fall due to a tantrum spiral.
More on creature cards, not all creature cards would draw from your FP. Some creature cards could arrive like migrants do, a band of mercenaries could arrive and ask for resources in return for fighting for you, these wouldn't draw from your FP. If your going to add magical creatures and summoning then creatures summoned by your Dwarven Wizard would only cost resources.
More on construction cards, it might be worth considering if the besiegers can attack them and destroy them. I'd like to be able to play wall cards which would act like those in MtG but there is no reason why defensive constructions like this shouldn't increase FM. "Has admired the fine battlements lately.".
It would mean more elements of DF would be present in the game: migrants, moods, recruiting, legendary constructions etc. It also adds a potential penalty for playing certain powerful cards.
Another idea. I like the idea of event cards, cards which don't necessarily attack only one side but that can have interesting effects on games. There could be an events deck separate from the players decks which contains the event cards themselves and player decks would have to contain a certain number of event triggers which when drawn force the player to draw and play an event card. Events could include floods, megabeasts, HFS and moree. Each card would last so many turns and then get shuffled back into the events deck. Event trigger cards would need to go somewhere, back into the players deck most likely, on the bottom perhaps?
Again events would add more elements from DF into the card game which might be nice.