The main problem with the pillars, for me, was the retcon they caused. They basically are our midiclorains - instead of the elements of harmony being something higher, they where actually just a defense mechanicsm that Starswirl created. Sorry, if you thought that it was something else.
On the topic of retcons, ever since the end of season 8 I have been bother by the fact that Tartarus is a fucking larger basement. It is not this mythical place that is partially in another dimension. Its an empty fucking room with a bunch of basement that ponies are in control of. It is a fucking prison andreally not an extrodinare one either. Talk about not delivering one expectation. It is not like that ever sicne we knew Tartarus was canon there has been fantazied to death by the fandom.
This goes for a lot of thing with these season that if they were anyway just gonna let us down then don't write about it.