Easy way to fix that is to make it so certain job types can't meld materia they can't use. Like prevent physical melee DPS from being able to meld Spell Speed, Intelligence, and Mind since those are stats incompatible with their job. Especially since melding the materia actually can't affect them. Tenacity and Piety also shouldn't be able to be melded onto anything but healer and tank gear because the description specifically says they're only applicable on those roles so the fact that they can be melded on anything seems like an oversight. If the devs are worried about true mechanical(and player error), preventing them from melding those things entirely is the first step to fixing that issue as well as more freedom with role-specific stats and materia.
All Gear accepts:
-Critical Hit/Critical Aim
-Direct Hit/Heavens' Eye
Physical DPS gear accepts:
-Skill Speed/Quickarm
Caster DPS gear accepts:
-Spell Speed
Healer gear accepts:
-Spell Speed
-Piety
Tank gear accepts:
-Skill Speed
-Tenacity
I'm on the fence about the STR/DEX/INT/MND/VIT materia since STR and VIT are currently used for tanks and HP optimization in high level content like Ultimate or progression through survival but.. even those two stats are extremely limited to just jewelry. Outside of tank jewelry, STR is a pointless materia and DEX/INT/MND see absolutely no use at any point in the game. Getting rid of the "STR Tank" was a poor decision imo because it was yet another choice/advantage players lost. One of many. But I'm not sure how to replace it..
EDIT: With Tenacity and Piety existing it's possible the devs might get rid of main stat materia and start making more Role Stats with materia. But the thought doesn't excite me because I know whatever stat it would be, it just wouldn't change gameplay all that much. FFXIV stat system is truly in a tough spot
But anyway point is that we won't be seeing BLMs with Quickarm V and DRGs with Craftman's Command VI if the devs simply nipped the issue in the bud by preventing it from happening at all, and lock materias to certain compatible roles/jobs. A change that doesn't affect gameplay in the slightest but does prevent melding that has no effect.