I'm not sure how this will apply to FF4A (noone has decoded that stuff yet, so I can't comment on the feasibility there), but this should help people try to work against an archaic system.
Despite being relatively archaic, the battle script system can be modded to react to a number of commands (like Steal/Sneak). This is very similar to FF6 where this is a common occurrence. You would have to specifically modify the list of counter/reaction list for this to work.
Another feature is that you can have enemies run special scripts due to the current status. FF4A definitely takes advantage of this (I'm not sure FF6 or FF5 does them in their scripts). So if a monster has Mute/Silence status, it could use an attack that ignores said status... like making a TinyMage to use the MomBomb's Explode spell while under Mute.
One of the unfortunate limitations of the system is that you can only have one attack per counter. It is impossible for example to execute the double hit as a counter. There are a few ways to work around this...
Cagnazzo's battle script involved modifying a variable that starts to trigger a different battle script sequence... now this can lend to a host of things...
1) The appearance of a specific enemy can trigger a different battle sequence altogether. This is "different" from having solo enemy or single group formations... For instance, I've written it so that the presence of the IceBeast would change the battle script run by a Chimera. In fact, if you wanted to, you could run a fixed-mix of counters that a monster can run.
If you have spent any time with the Soldier-Officer battle script (the save Rydia boss battle), the "Provoke" spell as I call it can allow you to do really cool things. In the battle, it is used to tell the Soldiers to attack. The Soldier's counter script "responds" to the Provoke spell, thus making them attack. I've played around with this extensively, to the point where a monster in a particular formation (specifically its current group) would run a specific counter attack. For example, if a monster is in group 1, it would Fight, but if the same monster is in group 2, it would cast some spell of sorts. This will require some tweaking of the counter code (it is easily moddable as said before) and it would increase the # of attacks possible by a monster group, w/o having to tweak around with the monster's speed/agility.
I may have forgotten a few things, but these are worth looking into in trying to expand a system which is ultimately very predictable, but you can get very creative in a very predictable system.