I think most of the problems I had while watching Sekirei Pure Engagement are caused by it being the second season. The story's not as fresh as it first was. The main character has already achieved something and some trump cards can't be played again without seeming repetitive.
The story hasn't changed much since the last season. Parts of the background story were revealed but that didn't change my perspective on the whole story much. I was sometimes annoyed by the action of the main character and some elements of this series got a bit old.
The animation is still good. Nothing jaw-dropping.
Pure Engagement definitely isn't better than the first season but I hope it's a necessary link between the first and the third season.