Do you hate or like Waller? *Spoilers Allowed*
I am indifferent to Waller, but what I really hate are her grey ideals necessary for "justice". I was seriously pissed when I realized that it was her who helped Riddler orchestrate the events in the Enemy Within. It just wasn't necessary enough for me to even go for her, at all. She just keeps acting like she has all the power and education to whatever she wants, yet her crimes are the ones she keeps to avoid her career being tarnished.
In my personal play through, I made sure not to make as much enemies as I can. I didn't get Tiffany arrested and took her as a protege, I convinced Gordon to get his old job back, released Catwoman, told Avesta to work at Wayne Enterprises, and I gave up Batman for Alfred. This was in my vigilante play through.