- Abilities and advances in jobs (as in Tactics system) based on personal story, kept in one's memory with reference to Echo.
- Advanced jobs are not necessarily stronger than less advanced, they just build from basics and pursue things more derivative or complex. A samurai of equal level will still likely beat an Ark Knight in a duel, unless dependent on his gear without a way to avoid an Arc Knight specialized in breaking such. But a Ark Knight will likely much more quickly and effectively turn the tide of a larger fight according to his ability set, and will make more (in terms of ability and gear effects) out of his own quests than a samurai would of his (save for perhaps duels with key personalities or characters, or certain conditions of large fights) due to his more abstract job parameters.
- There is a total amount of memory that a person can keep. But one can start replacing things and may even go back in his memory to attempt new pursuits.
- A class is not the end-all of one's potential abilities. It simply shapes how one will deal with an encounter and therefore what one will learn from it. This learning can eventually be shaped into one's own style or niche of a class, or job, or even an advanced job. (Though it is likely that these unique features will be carried over, at least in general trait, from your time prior to reaching the advanced job, rather than being learned after reaching it.)
Something like that. If possible I'd rather avoid a universal skill-tree in favor of something more individual. People may complain, but as long as they use the tools they've made for themselves well, they should be balanced. The things they don't... can fade beyond memory and be replaced.
If I'm an Arc Knight, it should say something about me as a player. If someone's going to face me and they hear that I've served with the Immortal's Merchant Guard and have been through wars against both beastman and imperials, that should also tell them something about what tricks I'm likely to have up my sleeves. If I'm a gladiator who soloed a level 40 group quest at level 30, it should say something about my persistence and precision. This of course requires increases to skill-gap and story and progression depth, but I don't think there's ever been a time where that's every been without benefit.