Here's a complicated suggestion, but I think it would be most appropriate given what has been provided before.
If any of you have not played Seiken Densetsu 3, well, you should go play it. One of the more interesting features of SD3 is when you have the God Beasts quest. The bosses and monsters in the areas that they are in to increase in level (with appropriate related stat changes) as soon as a god beast dies.
A similar concept could be accomplished in here... increasing the monster's levels and stats (probably using some sort of multiplier or table) when events are accomplished. These could be in the form or getting another character back or killing a boss, such as the 8 dragons, or even treasure chests like the Gem Box/Soul of Thalmasa. In that way, you can allow for going in any direction you would want to (like in CT... and a CT hack would stand to gain a lot from this concept) w/o forcing a particular/linear route and still manage something useful.
However, accomplishing this would most likely expand the monster bits (to either have certain monsters opt in/out of this system or have a degree of scaling from this method). So, it would be possible to run the Tower of Kefka with the bare minimum of 4 characters but also become scale to be harder when the whole complement of characters and other things are accomplished.
Not really sure why or where this would be appropriate, but it seems like this could be handled by a battle script on the affected monsters that bumps the desired attributes based on the chosen variable. This could be overt, and come with the a dialog or animation (say, as with barrier change) or silent, as preferred.
This would remove the need to make a bunch of formations.
If it's something desired
in general, the modification script could simply be inserted with an option to turn it off based on formation or event.
I don't like the idea of enemies leveling to match the party, but this could even allow that.
If the Ragnarok Morph transformation data isn't already claimed for something else, that data could be swiped to adjust what changes occur due to level. (e.g. 1=HP modifies, 2=HP modifies faster, 4=Add new HP to current, 8=MP modifies, 16=MP modifies faster, 32=Add new MP to current, 64=Att up, 128=Def up) This level-up data could be used in that script as well as in skills such as Brave or Old, should such be desired.
(Unrelated aside- have you considered consolidating the Mtek bio effect with the Tool Bio-Blaster? They conceptually share visual and in-game effects.
If there's some way that MTek status can simply bump up effective magic power, an increased effect is rather automatic.
I also like the notion of level mattering only little in MTek effects, with magical stats mattering a great deal
more. Also like the idea that the MTek effects tend to penetrate magical defenses as a rule. (no reflect, ignores all or half of a target's M. Def) Upshot would be MTek being nasty in the beginning, as intended, while staying useful throughout the game.
A spell/effect that allows resistances to be added up would be welcome. Yes, I realize you're full up.)
We have EVEN MORE themes now, but some old ones are gone...