This show was amazing for the first 2 seasons.
**SPOILER ALERT**
Personally I feel that the death of Emma Hill was the single biggest mistake of this series, and the loss of such a strong supporting antagonist led to this show's eventual downfall.
Even when Season 2 started to get a little rocky, (with the whole " Korbin" cult), her calculating, undaunted presence infused Joe's story with a wildcard element, I think chiefly because of her loyalty and resourcefulness, not to mention her being the last surviving member of the original cult from Season 1.
Even with Mandy, it felt like Joe had finally found his purpose, and a reason to nurture his ravaged human side, and for the first time...
NOT for himself (thus ridding himself of his narcissistic side, which brought about his downfall in S1), but for others around him he TRULY cared about enough to influence him for the better.
His character arc would have been so much more intriguing, diverse and complex had the writers deviated from the expected norm established in Season 1, which entailed the deaths of prominent characters towards the season finale. This did NOT have to be a recurrent rule.
Not to mention the introduction of different dimensions along which the series could have progressed as a result, chiefly the way in which Ryan Hardy would be forced to look at Joe, no longer as the serial killer he had so comfortably established in the recesses of his mind, but suddenly a man with a soul, and loved ones, drawing a painfully copious of parallels with Ryan's own life, particularly as this would also open avenues for Joe to start taking more risks to protect the two people who truly share a mutual loving bond with him in a world that would otherwise collectively shun him.
In other words, it would just be interesting to have witnessed a gradual sprouting of humanity within the most inhumane group of killers to have existed in memory, and the subsequent contrast in the way scene cuts would reveal the FBI to view them as soulless fugitives to be caught no matter what, while on the other side of the coin, the trio grow closer and develop human characteristics, perhaps even feud with Lily Gray's cult, who would represent a battle with their former wickedness.
The little dialogue in the car after they escape from Gray's cult is particularly significant in that regard, where Joe remarks "She's (Lily) a bit of a drama queen!" and Emma laughs, as it offers fleeting insight into what such a plot dynamic would have looked like onscreen.
I think the implications of such a synoptic variation would include:
Joe not mourning over his ex-wife or the life he had lost; this would eliminate potential for a LOT of lazily composed plot holes, wherein Joe is overcome with mental paralysis in the presence of Claire Matthews, his ex-wife, as he has moved on and is content with his new "family".
Lily Gray's cult being alive would allow for a three-way confrontation, and the effect of the intertwining would drastically reduce the monotony of the plot.
Opportunities to further develop strong characters like Emma into sources for fresher plot progression.
Avoiding repetition of previous seasons, like when Joe remade a cult in Season 2. There is no necessity to recreate past elements, a new season should focus on a new story.
In conclusion, I think the series was great until it started heavily relying on replications of previously contrived plots in a different context with newer characters.
It executed its original ideas amazingly well, but after they ran out of them, it felt hollow watching a series just repeat what it was known for over and over again.