Absolutely not. I don't think I could relate with him and love him so much if he wasn't flawed in the ways that he is.
I've discussed my thoughts on most of your questions (extensively) in another post (>>14120). It is a bit tl;dr so I'll try to answer a few of your questions more briefly here, too.
>What would be the difference between ignoring your waifu's flaws as opposed to accepting your waifu's flaws?
I see these as two extremely different things. Ignoring it is just that - ignoring that it exists. I'd consider acceptance as something that is more helping and giving, if it makes any sense. Not resigned exactly but wanting to help out and not necessarily change things, but maybe be the strength where that weakness is in your waifu's life. For instance, I've said before that Keisuke is kind of stubborn and he gets his mind set on things that aren't quite feasible a lot of the time, so I'd like to be (and often am) the voice of reason.
>Do you think your waifu's flaws can be turned into strengths, provided if she has any? Or is it just up to the individual's perspective?
I think there's a lot of that, too. A lot of people dismiss Keisuke as...er, well, a bad person, and I don't think they are wrong in doing so, honestly, as he did do some truly horrible things. And there are many people who call him spineless, a coward, weak. I'd object to those but I understand where they'd get that idea. I don't see cowardice in any of the things that he did and actually strength, but I know that it's just my view on the situation.
Most of the rest I feel like I'd be repeating myself too much, but as imperfect as Keisuke is, he's the "perfect" one for me, so to speak, faults and all.