First thing I'll be honest with is that she has been idealized, and with this I mean that it is really hard, in fact harder than most characters to define and see her flaws.
However, I know, and she does too, what her flaws are. Nobody is perfect after all, and even if she's looking to be that one perfect person, that one person everyone expects her to be, that one person that will save everyone eventually.
And I know better than anyone else these flaws.. since I will be the being avoiding others to get the upper hand thanks to those flaws
She is over-caring. She will do anything to save people and help them. And when I say people it means everyone needing help. Sicks, homeless ones, the list is huge. While it may look like a flaw for many people for me it isn't and I love to think about the times when I'll follow her and help them do so.
The only other flaw I can think of but which is the bigger one is her inner burning rage.
Nausicaä, is, as I said, over-caring. She cares for things so much insults, anything provoked by malevolent beings and people will make her go insane, more is the crime horrific more is her hatred. There are both those moments in the manga and in the anime, really impressive which also drives me mad anytime I look at them. I still have to say the one is the anime is way more impressive, since she had to pay an even greater price, and she did killed people something she thought she'd never do. She'll feel so much ashamed and sad about it she'll swear off killings for ever and will do anything to avoid harm by any mean.
While she still fight afterwards, point is that she never kill anybody else, this is a point I gotta insist on ; she worked paste that nightmare and fulfilled her wish.
Something I felt so proud of and happy for her.
For me, I already know what I will do ; fight physically for what she can't and won't do. My will is not to kill people, but is to protect her against anything that might harm her. I'm indeed that warrior, that knight in shining armor tales talk of so much. You could give me shit for this, and while I'd answer you this is only because I met her so soon, I'd say you're right.
But why would I stop this dream ? Fairy tales are that good for a reason after all.
Let's live it and bring it to life.
That's it. My waifu, while being one of the best person in the world, isn't perfect. Could one say people are perfect when they complete each others ? I strongly believe so.