Best way I can think of is FF2, but havnt played that since it was re-released as part of Origins for PS1. Don't remember exactly but when leveling your skills didn't other skills decrease as you leveled another skill. So as you got more proficient with currect weapon, the other would decrease. Think it was every 2 lvls gained, 1 lvl decreased? Could be wrong here its been so long.
I don't think skills decreased at all in FF2. Been a long time for me, too, though, so I may be wrong. Vagrant Story had a level/delevel balance system in place, and it worked pretty well.
That said, I'll be pretty upset if they put in a "skill atrophy" system. It'd make maintaining your character's balance a nightmare. "/p <Austreven> I absolutely can't cast Raise, 'cause if I get a skillup it'll drop my Y skill level that I need for Z job. Sorry, guys."
Also note: If this system is a more refined version of the system in FF2, I'll be really **** happy. That system was a brilliant concept, but the balance was terrible. If they sorted the balance out, it'd rock as the base character advancement mechanic for an MMO.