In the end I feel like most of us are suggesting the same thing with really small differences, and the 3 bigger systems I'm seeing thrown around here could be combined into a single one without really destroying the point of any of them.
Let's start by taking Kuro's system:
Specialize in specific jobs, with the option to choose how to specialize within the skill/talent tree.
If we make it so in order to be able to unlock a specific specialization path, you need to have leveled some other classes too, we're integrating the FFT system that people seem to want.
If instead of making the base classes simply spec into two or three paths, we make a lot of specs per class (with jobs overlapping, but their playstyles being different), we're integrating the crown system that's being suggested around.
The end result is something like this:
IMAGE: http://i53.tinypic.com/2uogoz7.jpg
To clarify:
1) The skills listed are some amongst many that you can choose by speccing into that job. You do not get all of them automatically, and you won't be able to get everything a job tree offers: http://i52.tinypic.com/vymlpe.jpg (Kuro's system)
2) The class icons listed next to the job trees are classes needed to unlock the job spec for the class (FFT system)
3) You can notice some job specs are repeated. They are all the same job, but their playstyles will be vastly different. A conjurer that specs into White Mage is a White Mage that uses direct healing spells, while a Thaumaturge that specializes into White Mage is a White Mage that uses healing over time spells. (Crown System, to an extent. The more jobs we repeat across the trees, the closer it'll be to this system)
What this adds to the flowchart that's flying around is: instead of simply asking yourself "what role do I want?" you can ask "what job do I want to perform it as?"
Let me know if this is a good compromise between the three systems.