While you have explained everything very well Kuroki, I stand by the fact that we are putting limitations on the character, and a lot at that. Which is fine in one way, but I am still of the mind that SE fixing Stats and Elemental Stats would accomplish some of what you state in your OP.

We know that each class has strengths in two of the Stats lets say for a Glad main stats as it stands would be VIT/STR Major stats and Dex as a third lets call it the minor stat. If we go your route and build a PLD then we would go VIT/STR and instead of Dex put some into Int for cure spells. If we went DRK then we would be doing STR/DEX Major and MND minor for increase in spell damage.

Let us now throw in working Elemental Stats (E.Stats) in the works, they would need to add light and dark into the mix (why they did not is beyond me) for this to work properly. They do not work as intended so instead of fixing it to work the way they were meant to work I would say have them increase your abilities. What I mean by this is that if you where a DRK you would put points into various E.Stats to increase your Dark spells, some in Dark, some in (suggestion) to increase BIO or Poison or what ever other dark spell you have. If you prefer PLD then you want to increase Light in your E.Stats to increase your Cure or what ever other light spell you have.

So similar to XI I guess, but you still have the option to use some of the other stuff that you learned from leveling/ranking up some other job. For example Marauder on STR/DEX since you have less points in Dex the abilities from a Marauder would be less so therefor you are not going to use them as much since they are not that effective. Let us throw in the E.Stats to make it even better, let us say you are using an ability such as Defender (which should of been a Gladadin ability to begin with) if it's E.Stat is Earth based and that E.Stat is lower because it does not do much for your DRK you can still use the ability but it will not be that great.

I do agree though that there should be some limitations, the classes are not that great but can become better, the specialization in my head is that instead of all abilities being able to be used across the board there will only be a subset that can be used and all others will be for certain classes specifically. For example Life Surge for Lancer can not be used by another class, if they do that as a way of Specializing the class then it will make you lean more towards that class if you like the skills/spells they have.

I don't really know how to fix it but I hope I was able to give you an idea of how your system can work Kuroki. I do not want to have the ability to change my Stats taken away and have predefined stats as a solution this is something that was done in XI.