This is the biggest problem regarding love for 2D characters, I feel. Rather, it's an issue for those who prefer to apply their waifu to the real-world - The folks who simply 'observe her from a distance' are exempt from this.
While fantasizing about conversation with her, it's difficult to say the difficult things - It's a denial of all of your negative traits (and rightfully so), and that's detrimental to loving somebody. They are entitled to their opinion. Of course, your waifu isn't real (obligatory ;_; face), but the notion of her being real is what you operate on when you imagine talking to her. And from there, the problem mushrooms - You think for her, essentially. Ergo, you are her, and she is you. She transforms from what she is to what you want her to be. She goes from waifu to a small fragment of your thought processes.
I simply don't like it because it makes my love for her feel like a sham. It makes me feel as if I'm only using her as a crutch, rather than loving her. The lack of material regarding her personality aside from the bare essentials, which I'm thankful for, I just wish I had the key points, y'know? But I digress.
The point being, it's an immense problem, with no solution in sight short of virtual reality. Biggest drawback of having a waifu, I'd say - 'Predetermined lines'.