I disagree; I don’t find Tomoyo perfect at all. She is quite flawed and her flaws make her deplorable in my eyes 
The fact that she’s so pushy whenever she believes in something and fails to see things from others perspectives is something I cannot accept from people.
And while (tomoyo after spoilers) Tomoyo After does definitely look into this negative aspect of hers, they approach it more from the aspect of “you’re wrong” instead of “the way you’re thinking is wrong” thus while putting a bit of perspective in her eyes, doesn’t necessarily solve the problem. Although I haven’t exactly finished TA quite yet so everything I have said just now could be bullshit
