as soon everyone have their character completed (all classes at level 50) everyone would be the same again with just different weapons.
Because you could equip nearly all relevant skills in FFXIV 1.0
Some skills were indisputably better than others, and there were enough slots to equip most of these "better skills". It was not a problem of "customisation" in itself. It could have been corrected simply by reducing the number of "slots" to equip skills, or by making more skills useful.

Don't confuse the concept with the execution.