I might just be going out on a limb here, but I have an idea. Just wanna say, I don't play Frantic Fusions very often, but I've seen a lot of people complaining about this. My idea is that for certain abilities, you could restrict those abilities to once per mon. An example of an ability that could be restricted is Regenerator. I've seen plenty of people complaining about having to deal with two or three Regenerator mons and I think this might be a solution to this problem. This allows for less viable abilities that should be allowed on multiple mons to be able to be used. This also means you don't have to allow all abilities to ability stack and you don't have to add a clause allowing only different abilities.
While I sort of agree with this (mostly that I think Regen needs to be nerfed a bit in this meta), I'd offer an alternative solution.
Restrict certain abilities to their native users
Idea being that while you don't completely eliminate teams comps like Regen cores from existence, you instead make them more predictable, and easier to counter as a result.
Say for instance Regenerator winds up restricted in this manner, and someone wants to fuse Great Tusk with Hydrapple.
New Stats: HP: 115, Atk: 151, Def: 158, SpA: 83, SpDef: 73, Spe: 98
Abilities: Protosynthesis, Supersweet Syrup, Sticky Hold,
Regenerator
Because Regen is now restricted to native mons, Tusk can't click Regenerator anymore.
But Hyrapple can
New Stats: HP: 106, Atk: 112, Def: 142, SpA: 133, SpDef: 93, Spe: 65
Abilities: Supersweet Syrup, Sticky Hold, Regenerator, Protosynthesis
While not as physically bulky, it still has much better Special bulk, and can still click Regenerator, making it a solid Regenvest Pivot. But with a glaring weakness to Ice.
So now Regenerator would be limited to the Slow family, Alomomola, Amoonguss, Hydrapple, Torn-Therian, Mienshao, Reuniclus, Klawf, and Cyclizar. And while the donors and the stats gained can vary, it's easier to slot in coverage to deal with the now more predictable Regen cores.