Let's face it, the world has gone to such crap that it needs to be rebuilt since they're pretty much living in hell now.
Why do I get the feeling that they started making 3.0 like it was in the teaser at the end of 2.0, but one day Anno just came running into the office about a year into production, high on god-knows what, and then declared 'Everybody, scrap everything! I...have an idea'
Back on topic though. 'Does Misato have any redeeming qualitites?' Let's weigh things up. She does refuse to kill Shinji despite Ritsuko all but screaming at her to do so. She does act coldly to him, however even that is arguable if you look at the perspective that, like Rei, she didn't want him to have to pilot the EVA ever again. She also made a point of locking the DSS choker to her password and nobody else's. She also changed her method of referring to him from 'Ikari Shinji' to just 'Shinji-kun' and was shown to be thinking of him throughout. I feel they made a point of NOT fleshing out Misato in this one to see why she is how she be revealed in 4.0, even Asuka is hinted as not hating him i.e. just wanting to see his face, seeming geniunely hurt when he raised a hand to her (personally I laughed though when Unit-13 took it's pimp hand to her) and also whilst kicking him initially, she did come back to the entry plug for him in the end and take him with her.
Bottom Line? Misato has been dented, yes, but not beyond repair. at the end of 3.0 we're basically where we were episode 24 in terms of Shinji's mental state. It's now with bated breath we see if Anno will finally show some mercy on him.
At least the manga has ended on a somewhat brighter note...