The issue with such a grind (for a grind is what it is) post level cap, is that you segregate newer jobs from well established jobs.
What do i mean? Well, right now, a new job only needs to hit the level cap and catch up on gear.
With your Merit System, i would need to hit cap, get gear AND grind for months to get the boosts which would be mandatory for raiding. And dont kid yourself, they would be mandatory, if they weren't required to raid, Raids would be made too easy by having them. If they balance around Merits, It just adds further gates to reaching even the first level of raiding.
It makes it difficult for new players to join established communities, as those established players with their long playtimes on their Jobs have a statistical advantage over the newer player, who would then exclude the newer player for being at a significant disadvantage.
Please don't take that as me being against customization. I would like to see some customization, However they cannot be stat upgrades or power boosts. We cannot have Time = Power. Especially when we get a few expansions in.
If anything, We need the Materia System modified to to take a customization role.