The main issue I have with the Job Crystal system as it stands right now, is that it doesn't really support role changes in a level sync environment, as we see with Arcanist -> Scholar. Specifically, just let the fairy do the work while the Scholar can just hit Cleric Stance and behave as an Arcanist all day. (This also doesn't get into the ability progression issues, such as the lack of status cure in places like Brayflox's Longstop. Round 1 went to White Mages here by far, until the Antidote change went in.)

What I'd personally like to see, is the Job Crystal basically overwrite the class progression and trait acquisition with its own line. So, to use Scholar as my poster child, you could have something like this happen (traits are in brackets):

1 - Ruin
2 - Physick
4 - Bio
4 - Summon (Eos)
6 - Aetherflow
8 - Energy Drain / [Aetherdam]
10 - Miasma
12 - Virus
14 - [Enhanced Mind I] / (Eos: Whispering Dawn)
15 - Summon II (Selene)
16 - [Enhanced Mind II]
18 - Leeches / Sustain
22 - Resurrection

and so on. I wouldn't personally do it exactly like that, as I consider it more of a bandaid approach, but that's not the point. My point is: mix in the important Scholar healing abilities at lower levels instead of enforcing it to be at the level acquired via the Job crystal. Some abilities (Leeches the big one) should be available roughly at the same time as other classes in the same role, if only so that they're each on a similar level at a given bracket of progression... if that made sense.