So you're thinking that along with the various class sections in the skills/traits UI (e.g. Polearm, Sword), SE would add another "Job" category that would display all of the jobs currently unlocked? This would certainly be more convenient than 'burying' each job within the class that unlocked it.
As to the assignment of restrictions to either the job or the class skills, I suppose it depends on whether there are going to be more jobs or classes. Either way means a fair bit of work when a new job or class is added. I suppose the simplest way is to identify (for each weaponskill/ability) which jobs it can be used for (positive identification) rather than listing the jobs it is restricted from (negative identification). In any case, as the game grows and more classes and jobs get added, progressively each new job will take more time to implement, since every weaponskill in the game has to be potentially looked it.
If each weaponskill lists jobs it can be equipped with, a new job designer simply looks through the list of weaponskills/abilities (across all weapon classes) and picks out those that fit the new job, and updates those weaponskills. Seems like the least painful option.
What would you think of varying the affinities of various classes to each job? Right now most abilities and skills seem to be around 80% effective used cross-class, or 90% with the correct affinity trait. So maybe a Paladin gets 100% affinity with sword traits, 90% with Axe, 70% with Conj Arms, etc. In this case a Paladin / Sword, using sword skills would be at 100% affinity, a Paladin / Axe using axe skills would be at 90% affinity. However, a Paladin / Sword using axe skills would be 80% affinity (for the cross class loss using axe skill as sword), or 90% if the axe affinity trait were added.
This could be used to balance the job / class combos against each other so that each has strengths / weaknesses compared to the others, preventing devolution to the point of people only playing the "best" class for each job.