I'll have to think more of this to give my own idea of how to fix things but, I think the only critique I have is that I don't think your system fixes the imbalance of melee vs. mage in the game. Melee will still be dominating because they are not losing stats every turn, while mages become sitting ducks after awhile. I'm also curious about where the GF summons and Draw/Cast fall into this whole deal because I feel they would still be better alternatives than sacrificing your own stats, by casting Junctioned Magic. I think you need to address a balance for those two applications to make the system you propose work.

As for the Draw 100 spells the first go around, I feel its still a bit imbalanced, especially with the above critique. Granted you have a good point about it not being of any use until after the battle, but I think its a bit imbalanced that after leaving Balamb Garden, I go into five battles, that only take five minutes top to complete, and now I suddenly have a really beefy Quistis and Squall who can coast until the end of the Dollet Mission if I stuck to melee and summons. I feel a much better alternative is to simply limit the amount of spells you can draw from a monster. Basically, a Bite Bug has 15 Spell charges of Blizzard I can draw from, and then after 15 are drawn between my party, we can't get anything out of him. This would drop battle time significantly while still creating a sense of accomplishment when you finally draw enough spells to make meaningful Junctions, and it would keep refinement as a viable option.