I'd also like to see new Blitzes, and a slight damage formula change where Vigor, Weapon power, and Hit% determine the final damage or enemy evasion.
That would be nice...
And speaking of changing some character skills, is there a possibility to change Runic to not only absorb the MP but to have a % chance based on Magic Defense % to randomly reflect casted magic spell?
I'd rather hope Runic doesn't rape your MP gain due to resistances instead. I'd rather have MP increases... like resistance = 50% more MP, immune = 75-100% more MP, and absorb = 100-200%.. then stick this to a monster that relies on said behavior (like Tower of Fanatics or Magitek Factory)
Change Lore to randomly not cost any MP--formula based on Magic Power and or Stamina.
How about allowing Lore in the Tower of Fanatics (including enemies to be able to cast said magic to be a true magic tower)?
Make Sketch actually useful? Maybe say if she successfully sketches a monster and casts a normal learnable magic spell it gives her an extra magic point or % increase in learning said spell?
That doesn't sound that useful... I'd say something like auto-doubling exp/gold (or item drop rate increase or something special along those lines) for the target that is copied...
Have one of Shadow's retort dog actions be replaced by a random Throw or a regular attack.
I'd limit the throw to a regular shuriken...
Remove "Summon" battle command and create "Geomancy" where the character of choice who has this skill--whether it be naturally obtained or through an item--can cast a random enemy skill/spell that doesn't make the character Berserk but it costs MP.
I'm kinda against the MP consumption there...
Have a map somewhere in the game that can randomly spawn ANY of the non-boss formations regardless if you fought that battle before.
Now that would be Veldt++.
Increase the ability to have more than 99 items.
Overpowered.

Create random "air" battle formations for when you are flying the Enterprise and or Falcon.
Should be optional/togglable IMO... but there should be more "water" battles so Water Rondo is possible (think FF6A's Leviathan).
Reduce the number of Chocobo stables, or increase the price significantly.
Stopped using these long ago... maybe add something special for finding them at least...
Create "item quest" NPCs. For example create some random NPC in Mobliz that asks if you have or can find "x" item and if you bring it to them they will give you "y" item. This would be a good way to distribute some rare and or powerful stuff.
More MMORPG stuff?... Meh

Item exchange NPC. Give the NPC 3 Tonics and get 1 Potion. Give 4 Tinctures to get 1 Ether. Give 2 X-Potions and 2 Ethers to get 1 Elixir. You get the idea.
Sounds like a borrowed idea from CT.... better than nothing I guess.
Expand the Colliseum to its own large island with its own mini town/village and shops.
That sounds like fun.
Create a monster rancher NPC that can allow the party to fight WoB formations that people might miss the first time through--IE Intangir etc.
That almost sounds like a variation of the other idea you put up... at this rate, the FF6A multi-battle garbage in itself is overpowered by comparison.
Some newer ideas..
Create a "random" elemental... so that the weapon deals random elemental damage on a target.. make it powered by your level or some cute formula (similar to the Atma Weapon).. and allow enemies to attack you the same way as well. If the enemy is immune to all elementals, make it non-elemental in this only case (unless you want it useless later on).
Create a variation of the game that has MP as a dependency. Treat 0 MP to instant death (a variation on the enemy attribute) on your own characters (it makes Rasp/Osmose more threatening in this game). Revival by Phoenix Downs will install a countdown timer until the target has at minimum 1 MP (make Osmose behave like FF4 at 0 MP) or dies automatically if MP is not recovered. Life1 will restore a sane amount of MP (10-15%), Life2 will restore 25-50%, and Life3 will restore 15-25%... Economizer must be removed or changed into something like the Regen Ring, except for MP... there are probably other things that need to be factored in properly (I can't think of them offhand...)
Soul Sabre would need to be revamped... make sane damage and up to 15% of that is converted into MP... or something like that.
Then again, these are probably tough to make happen.. but meh.. I had cooler ones posted before.. I think.