"[...]my biggest problem is the idea of making Yui an innocent. She's totally not."
I fully agree on this...

"I'd even go so far as to say that she's the mastermind behind everything that happens in canon."
...but not on this. The whole NEG storyline is to complicated to actually have been masterminded by anybody that is not part of what is happening and can direct the "plan" when something unexpected happens. But than again the whole premise of NGE has a huge plot hole in it.