It's an interesting choice. They're still sticking to the "charismatic weirdo" formula, but switching from cynical sociopath to sincere zealot is enough to ensure that they're kept distinct. Not an inobvious one, granted- it's basically what Nolan did between Dark Knight and Dark Knight Rises, although while Seed doesn't quite measure to Pagan Min, he has a better showing than Bane did against the Joker. I think the sub-bosses are definitely an improvement; the sub-bosses in 4 didn't really make an appearance outside of their specific missions, and the only one who made much impression was Noore, but in 5 they do more to define their respective regions, and you get a sense of them as characters, albeit somewhat thinly-drawn ones, rather than just as roles within the villains apparatus. (There's an interview with Alan Moore were he notes that the superheroes of the Silver Age were basically two-dimensional, but that was a step-up of one whole dimension over the Golden Age; something like that applies.)
It would have been interesting if they'd committed to a more grounded version of the cult, which is to say, made them fundamentalist white supremacists, the sort of people who might actually try to start a theocratic microstate somewhere out on the plains, rather than what amounts to a militarised version of the Mansion Family, but I can see why that potato might be a little hot for a triple-AAA title. Plus, the developers seem pretty convinced that every entry in the series needs to have weird psychedelic sequences, and I guess this keeps it thematically coherent.