For magic, I generally halved the total bonus given by magic to every stat by half. This may sound extreme, but the vanilla game was quite easy, and once again, the increase in character stats help mitigate the loss.
One of the few stat bonuses I raised was the bonuses to Speed stat. Most early game spells now give a greater bonus to Speed. This is in order to provide greater benefit to a character with a Speed-J, but no Str-J or Mag-J. I also slightly lowered the default speed stat of each character to compensate for this bonus.
Beyond that, almost every stat bonus was altered either up or down. The main variation I made was to status and elemental bonuses. Now a lot more support magic will offer a variety of defenses, allowing for more options than simply an all or nothing junction with specific status and elemental magic.
I also lowered the draw resistance of every spell. This will save some time, and prevent you from only being able to successfully draw with the character with the highest magic stat.
As of version 1.1, I have rebalanced the stat bonuses gained from junctioning magic. In order to provide some much needed structure to the overall quality of junctioned spells, each spell is now arranged into a tiered system.
There are 6 tiers total, and the magic is roughly arranged according to how early you gain access to it, with 1 being the earliest, such as fire and cure, and 6 being the latest, flare and full-life. Generally speaking, a spell of one tier will always be inferior to a spell of a tier above it. While there is a small amount of overlap, every tier 4 spell will almost invariably provide a much better bonus to every stat than a tier 2 spell.
Within each tier, magic has been further arranged into 2 categories, attack and defense magic, usually with three spells for each category. Attack spells provide a greater bonus to Strength, Magic, and Speed. Defense spells provide a greater bonus to Vitality, Spirit, and Evade.
As an example, in tier 3, the attack spells are Fira, Blizzara, and Thundara. Thundara is the best spell in tier 3 to equip to the three attack stats, followed by Blizzara then Fira. This structure harmonizes with the GFs, who are already divided by these same stats, in order to offer strategy to how you set up your team. Instead of finding the most optimal spell for each stat, you must choose which stat you want to favor most, and which one you favor least. This is also true for the defense magic.
My goal with this design is to help foster a strategic approach to junctioning, as well as minimize the game-altering junction bonuses from early game spells (such as protect and shell). Also, each spell still maintains a degree of variety and individuality that shouldn't eliminate the sense of satisfaction when acquiring a new spell.