Create a script that changes the stats of a skill? Sounds extremely complicated for us n00bs. It would be more "non-scripter" friendly to just be able to determine what skills are linked (I mean, what skills are replaced by others with enough uses) and then go in and create many copies of that skill, changing their power, accuracy, adding effects by onesies and twosies. Make a bunch of Cross Slash copies, and make each more powerful than the last, or have higher versions add extra states, or add elemental bonuses, or whatever. Then, link them in the script configuration. I'm sure it would be an easier script to make and use. It's simple, and very flexible.
As for the whole "branching" thing, how the frak would that work out?
Edit: BTY, Cyclope, that 'experience atrophy' idea is utterly brilliant.