So unfortunately I am scrapping the card game mechanic in favor of a more real time type of battle system. It all works only in my head as of now so that's not set in stone.
Have you considered something like Final Fantasy 12's Gambit system for battling?
http://finalfantasy.wikia.com/wiki/GambitsYou essentially construct a primitive AI by combining Commands with basic Criteria and then the characters perform actions based on the priority that you list them. For example...
-If below 50% Health = Heal
-Target enemy with Fire weakness = Fire
-Target enemy with highes HP = Attack
So pretty much the same set up as old RPG AI systems but you have the option to mix and match actions and change setups on the fly.
Rather than directly controling the character you would take a back seat and manage their response to a situation. Which personally I feel is a good match for a Monster Training RPG.
Some mosters would follow orders directly, where as some more toublesome monsters could stray from their AI set up on occasions. A timid monster might heal more than they have to, whilst an angry monster might lash out with powerful attacks when not needed.
Players could set up various 'AI builds' for each monster (Attack, Defence, Buff, Debuff, Healer etc), and then flick between tactics depending on the battle. Kind of like how a Sport Managment Sim plays differently to a Standard Sport Sim.
And if you wanted to keep to your procedural design there is no reason why all the Commands and Criteras couldn't be randomly generated.
Some monsters might have the 'if below 50% HP' command, where as others it might be 'if below 46% HP' or 'if below 31% HP'. You would have to build your monsters AI based on what commands they had access to.
As the monsters level up not only do they get stronger, but you also gain more AI options and flexability.