I won't say I've ever felt like screaming at a character in an anime, but I'll play along with the idea.
The main character in Chaos;HEAd does a few pretty stupid things, but it didn't make the show bad until the end, really. The character's stupidity didn't hurt the show.
Now, as for School Days, I thought it was horrible because of the characters' lack of intelligence. I honestly do not see why that show is so popular. It's seriously not realistic in any way, and the characters are just so excruciatingly annoying all the way through. I honestly think that anyone who recognizes real life in that anime must be socially retarded, and I'm quite the introvert myself, saying that.
Shounen jump characters often do stupid things that make me really want to facepalm as well. But that's to be expected, since it's fun for the younger ones.
Well,if I were Makoto,and followed up his path,I wouldn't had the idea of being a super-sexy incripted in my head.If I would be a pimp at least I would take care of all girls,especially Sekai(who was my favorite).
Well,the ending was gross.I mean,really really gross.To be read as"Very sick,convulted,weird and gross".
As for shounen jump characters,all that I can say is this.
Strategist:Uhmm,doing that will cause a slaughter,so it is better not to go in.It's better to lose just one than 14194.Plus,we have no possible way of winning.
SJ main lead:Uhm,friendship?We go in.*battles,everyone's dead,even he,but miraculosly he comes back to life,beats the crap out of everyone,finds a cure for everybody with a lame plot device,and then proudly says"I told you so".*