So, as an idea, maybe instead of having characters earn JP ponts, or maybe on top of it, have it so you can equip a stone of various quality that can basically be a "battery" of JP. That way when you start a new character, if you say bought a "JP stone (s)" and filled it up you can instantly have 20 bonus JP for one character. Or if say you bought the expensive large version you get 50 jp. The stones being one time use in themselves.
This way you incentivize keeping older characters in the party beyond just being a quicker way to level newer characters, and have them still progress the party even when max level. Or if you just aren't ready to move on to the next generation but have maxed characters with the skills you wanted, they again can still help the next generation with a headstart beyond just breeding.
The learning system is interesting, but beyond the rarity of the JP trait and just how limiting the learning system is currently; I feel this might be a way to make the JP system more meaningful without maybe having to rework to much hopefully.