In theory I can see where this line of arguementation comes from.
Lore-wise, the point I'd raise in response is that FEV was imprecise even for The Master: the vast majority of test subjects didn't get vatted properly, that's exactly why the discovery of Vault 13 is so important to The Master. Even if Gen 2s will never be as perfected as Gen 1s, the point still remains that creating such a clear cut divide with one being the "Smart" supermutants and one being the "Dumb/Evil" supermutants feels like it doesn't fit in well with the fact that even among the Master's creations there was no consistency, and plenty of them turned out rough, or with unexpected side effects he couldn't control.
However disregarding lore for a moment and solely talk about story-telling, I feel like "These people you're fighting are too dumb to know what's good for them, and are easily swayed by propaganda" is kinda a cheap story beat. There are infinitely more interesting stories you could tell about how experiences shape culture, and how even seemingly arbritrary differences in history can shape an entire culture's way of seeing the world, and the differences in Generations of Mutants has this clear potential.
Slowly finding out that the Enclave accidentally created the 2nd Gens using Slave Miners simply to recover FEV in the second game was a major high point of the plot for me. Even the fact that the Supermutant Boss has a son waiting for him who he was ripped away from adds a lot of humanisation to what pretty much only exists to provide a high-level dungeon for players to go through.
Story-wise the "2nd Gens follow Tabitha because they're stupid" feels like a missed opportunity. It creates an inherent divide between generations of Supermutants based on how they were created, and instead of doing something interesting and humanising to the Mutants, instead creates what seems like a shallow and deterministic view of human nature "These people do this becaue they're dumb and evil because of the way they were created" feels more like a World of Warcraft plotline than a Fallout one.