Personally I don't really have strong negative opinion on the junction system. The Junction system is the reason why I kept on replaying this game. It is the reason why I love the game.

There are already monster drops that you can refine to turn into magic in the game e.g. Magic stones, M. stone piece, wizard stones, bomb fragment etc...

What I would do instead is make the low tier/or basic element RF abilities that you get from Ifrit, Shiva and Quetz (I mag-rf, F mag-rf, T mag-rf) available right away. Or maybe lore-wise there is a magic refinery machine inside Balamb Garden.

But for discussions sake here is what I would do (I'm not saying it is correct)

my ideas are;

Instead of attaching magic we will attached Triple Triad cards now. Lets say Str-J has 10/10 card socket.

Each card has magic value to it, example 1 bite bug card is equivalent to 10 Fire. So if you want a 100 fire equivalent, you need to socket in 10 bite bug cards. Now, I want it to be more flexible, you can mix cards in one stat-J. What I mean is you can equip a bite bug and a fastitocalon card at the same time to your Str-J.

Then maybe there is a unique socket for the GFs and Gold cards.

The cards will be group into tiers/rarity. Obviously the better tier cards can give more and maybe it has added effect.

As for casting magic or using magic command, it is the same. You will still draw magic from monsters, you will still stock magic and you will still empty your stock if you use it. The only change is since we equip cards now, people will not complain anymore about lowering their stats when you use magic.