Persona fanbase can be a vicious and defensive one. They like their Persona games a certain style, but will support the IP regardless of what direction it takes. Devs know this and try to stay faithful to what makes the series great, building on each new entry, which in turn keeps fans coming back for more. Square and Atlus aren't in the same position when it comes to what fans want and expect. Square has the luxury to take the hate it gets and brush it off while moving into the next thing. Atlus tries to stay faithful to fans since alot of what they put out in the past was niche and catered to a small group. They didn't have the luxury to brush off outcry thinking they'd get continuous support.
I hope that makes sense. This is just my perspective though.
Doesn't FFXIII VS becoming FFXV contradict this?