I think it is not the question what it can not change but the question of what can a Merit/Modification system can change using what we already have.
For example..
a Machinist Modification tree could progress can provide options on how they want to change their skills.
Gauss Barrel Modifications choice, once unlocked, can be
1) Give electric shock DoT effect on attacks with it stacking up to 5 for stronger effect per stack.
2) Remove cast and return auto attack with Gauss barrel equipped allwoing players to be mobile again with Gauss Barrel Active but reduce the damage a bit in exchange for getting auto attack back.
3) Increase the damage increase of Gauss barrel even more.
Ammo modification can be
1) incendiary ammo - perform a burn DoT effect.
2) Armor Piercing Ammo - a more direct damage increase.
Rook turret modification can be
1) Modificed Rook Turret - Stronger version of Rook turret.
2) Pawn Turrets - Give all members in the party a mini-turret (noticed by a buff on them) that attacks their target. Alone it is weaker than Rook but if all 4 members can stay alive it can be stronger.
Bishop Turret
1) Modified Bishop Turret - A slightly stronger version of Bishop with a larger AoE range.
2) Knight Turret - does slightly more damage than Modified Bishop Turret but sacrifice their 360 degree AoE for a 90 degree AoE attack.
The merit/modification system can also be the means to allow Summoner to access the other Primal Egi as they have established Summoner's are restriected to a limited number of summons lore wise being 3 (1 tank, 1 melee, and 1 range).
Melee Summon - Default is Ifrit-egi
1) Ravana Egi
2) Default Carbuncle
3) Ruby Carbuncle
Range Summon - Default Garuda-egi
1) leviathan egi
2) Good King Moggle Mog egi
3) Default Carbuncle
Tank Summon - Default Titan egi
1) Default Carbuncle
2) Obsidian Carbuncle
3) Odin egi
etc etc etc.
Another matter would be the leveling of the Merit system as it is the question should it be a separate leveling system so the max level remains lvl 60 or would players begin to obtain points for the Merit/Modification system once lvl 61+ and the unlock of the Merit/Modification system in each Job remain separate for each job. Unlocking only sections of the Merit/Modification tree as players complete their Job Quests.