Sure, Shinji from Neon Genesis
Sure I don't like him either, but the pure amount of hate he gets is abnormal. Some say he's a coward and a weakling and that's true to an extent.... but he's a 14 year old nerd for pete's sake. He's not macho-rambo, bring-em-on super boy. He's just an average young teenager, shyer and more emotionally sensitive than most. Yes he breaks down - but after all the crap he goes through many would too. Shinji doesn't fit the standard "hero boy" mould that most anime and manga try to cram down your throat, and for that, I like him as a character.
95% of all manga and anime is pure and utter garbage. Cliche, run of the mill dross that you can predict miles away. Hey guess what, you know Naruto? Think he dies at ANY point in the manga? Because if you do you're an idiot. Naruto is NOT going to die in the manga NAMED after him for kids and teenagers. In BLEACH, Ichigo is NOT going to die. Naruto and Bleach lack any tension at all, because it's so painfully predictable. Every time either is in an impossible spot, Naruto will pull more stamina/chakra out of his ass and Ichigo will pull another power jump out of his rear-end. Or someone will come and save them, or the enemy will "have to go away for a while". Both.....are.....so......boring.
At least with NGE, characters DIED, protagonists could turn into antagonists, almost everyone was emotionally screwed up and although it was predictable and run of the mill for the first half of the anime, it quickly took a turn down dark and weird street and was all the better for it. The movie was a complete mind-screw too. Which was refreshing.
But this isn't a rant on how bad most anime and manga is, it's a rant on which characters I want to defend. So in no particular order:
Otacon from MGS - because he might be a whiner, but he's a computer scientist. Not grim soldier guy.
I'm not sure if Zarniwoop was hated very much in HHGTTG, mostly because he was in there for about all of 2 chapters, but he's portrayed as a villian, when in fact he's just trying to get to the truth.
Oh and again, a lot of people hate him, but Bernard Marx from Brave New World. Oh.... hm. Yeah I don't like him much either. So forget about him. Some seem to hate Mond a lot too, but I thought he was, by far, the most sane, intelligent and likeable character in that whole book.