Skill trees can be good, but on the right conditions, and I don't think FFXIV offers the right conditions for it.

There are, in my opinion, two important points that we need to consider when dealing with a skill tree system:

1) Do we have separate role oriented skill trees or not? If yes, can we make a build that allows us to mix them or not?
-If we have well defined skill trees and cannot mix them, then it ends up the same as having 3 different jobs that can use the same weapon. So just make new jobs and no need for skill trees with the system we have. However the current system defines the jobs by the weapons used. An option would be to base jobs only on job stones like SMN/SCH does.
-If we have one big skill tree with offensive, defensive and healing skills or well defined skill trees that we are free to pick from to mix like we want, then we need to take into consideration optimization and out of the norm builds. In a game where there is a good balance of PvP and PvE, having something different from the masses can be good, the element of surprise might help win a fight and have the flexibility to quickly react to surprise elements coming from the other players. In a heavily PvE game like FFXIV, this will not work. If you are not optimized for the role you are taking in the party, you are pretty much giving up your place to someone who can do better just because he has the better build. FFXIV has some PvP, but we have extra PvP abilities that act like a skill tree.

2) Are we allowed to change freely our skill tree build or not?
-If we cannot change our choices or need an item to change it, having separate jobs sounds like a better option for me (and it's back to first part of point 1: different jobs sharing the same weapon).
-If we can freely change, we will surely need to save them to be able to switch easily (like we do for gear sets). Problem is, that creates a lot of extra data. Our characters are already heavily loaded with data (classes level and attributes distribution, gear sets, hotbars setup, inventory and so on). It's not impossible but will require to give up on other type of data or wait for a more optimized system (since the dev. team said they were looking at optimizing item data to be able to increase inventory space)

So yeah, although skill trees can be fun, I highly doubt they will be useful in a game like FFXIV.