The base concept:
Skills are unlocked in one of two ways, with this. The first is the current method of reaching a specific level and getting specific skills.
The second are skills categorized as threshold skills- these skills all become available, at once, at a specific level threshold, of which there are multiple. Once you reach the threshold level, you gain access to all threshold skills between that threshold and the next.

How they work:
Threshold skills, unlike static unlocks, would not be affected by level sync, much like Role skills.
This is balanced out by Threshold skills being controlled by an AP system, requiring you to set what skills you want to be able to access up to your AP limit.
The AP limit is what would be affected by level sync- As your level increases, so does your AP, up until you can access all of the prior threshold skills. When level synced, it reverts to what it would have been at the synced level.

How do you ensure people know what to use?
That's what the first method of unlocks is for. The details would be up to the developers' prejudice, but core skills like combo skills and important job mechanics, such as gauge mechanics, would be controlled by level sync and unlocked at their respective levels, and disabled when synced to below that level. You would never and could not ever have a moveset that allows your job to function as it is intended to at its base level, to prevent trolls who would intentionally disable core skills, or worse, all of them.