To be honest I actually hate the "skill tree" systems (and similar). Certainly for a post level cap / "merit point" (XI haters gonna hate) system it works but for the core elements of the game, I would much rather set skills learned at the associated levels (as is).

As soon as a new battle mechanic shows up, and you discover that a certain skill is required / more useful in that particular content, it kind of forces you to rework your points and what not...

Another negative with skill tree systems is you have to allocate your points as you go / select your skills and when you are just levelling a job. Sometimes the description of the skill is either underwhelming over overwhelming (the description says "causes huge rediculous amounts of massive aoe damage" but it is really extremely weak compared to one that says "deals single target damage"). When you are a newbie leveling up, you select the skill that sounds like it would be the most useful then later finding out that it is garbage.

Keep every class/job for everyone the same, until level cap. After you hit level cap you can look at doing some customization.