The Point Allotment makes no sense without the Physical Levels and the Jobs too make it kind of useless to have a Point System when each Job needs to have certain stats in order for it to work effectively.

So it saddens me to say it the only real use of the Classes is that sort of base element needed to obtain the Jobs. Sighs... I miss the Old Thaumaturgy... the Job System butchered it so badly....
Yeah, point allotment is dumb in my opinion. It's extremely limited and every class has 2 main stats that they need, so just pump them into those two stats. I guess it's nice for those people that want to be different.

There's still use in classes, but it really does depend on the class. With the large rebalancing coming in 2.0, who knows what will be good and what won't. For your example, Thaumaturge was often preferred over Black Mage because of Sacred Prism + Sanguine Rite... and a lot of people didn't want to play Black Mage due to the lack of White Magic (Raise, Cure).