I wouldn't mind seeing compartmentalized / modular cases, but since they're not standard, few manufacturers will risk making parts for them. Unless you make non standard cases that still adhere to some ATX measurements and will fit ATX components without modifications. But does that lead to something like the Level X case that's prohibitively expensive?
I'm not sure how you can effectively separate the CPU and card airflow with a generic case. Suppose you have a partition wall between the two. It doesn't have to touch the board, but it does need to be relatively close to it for airflow separation. How can you assure it will fit the majority of motherboards without touching circuitry, VRMs, heatsinks and pipes, etc. It'd have to be some sort of custom work where the end-user has to cut away from the partition to fit their own board.
But ultimately, if you're separating the cards from the CPU, why would you want the fan on top of the card at that point? It would be right up against the partition, and that doesn't make sense to me. Unless you're proposing departure from the ATX motherboard, which would make this whole thing moot.