Instead of Gestalt, how about free Variant Multiclass for everything with a stat block?

[Reksew_Trebla]

So everything, even class features like Animal Companions, gets Variant Multiclass from Pathfinder Unchained, without having to trade feats for it. If the creature has more than 20 HD, they will start getting an additional VMC, also for free, to make up for the fact that they already got the full effects of VMC for the first 20 HD. If a creature somehow has more than 40 HD, again, they will gain another VMC for free, and so on and so forth for every multiple of 20 HD.

I will allow 3 extra options, a variant of Paladin, Rogue, and Cavalier, based off of Antipaladin, Ninja, and Samurai, trading the gained class features of original VMC options with those of the Alternate Class equivalents. I will also allow some archetypes to be applied on the VMC, as long as it actually works appropriately. For example, I would allow the Wildblooded archetype of Sorcerer, since it doesn’t cause any issues.

So how does this sound? It allows the idea of Gestalt, without the muddy rules of some prestige classes not being allowed, and the whole not knowing how to change the CR of NPCs that are also Gestalt, as in this case, every monster gains this benefit.

[Anarchy_Kanya]

I'd rather take gestalt.

[deuxhero]

Problem is variant multiclass options are all wildly imbalanced. Many are just absolutely garbage (Paladin, all full casters except Sorcerer).

[avr]

Sounds like a lot of work for the GM in prep and a fair bit even in play. Gestalt would be worse admittedly, but PF can push the limits of what's acceptable for me as a GM even without either of those.

[Lelomenia]

I like the concept; VMC is a cool concept but generally not worth the feat price tag., Problem is a lot of the VMC options are worthless and worse, uninteresting. Because of the lack of balance between the options, they’ll probably go toward the mechanically relevant ones instead of anything RP appropriate. I actually like Wizard VMC.

And it seems excessive to give VMC classes to animals and swarms and slimes and probably skeletons etc