You know, if you're saying that all 3D girls are horrible, conniving bitches, then you obviously haven't met enough girls in your lifetime, or you've met--or gone after--the wrong sort.
As the OP said, he has friends who are girls that have similar interests to him and who make him laugh. Well, there you go, we aren't all horrible nasty creatures, are we?
The problem with generalising about high-school-aged people, is that you're really seeing the worst of the worst in anyone. Teenage years are just plain weird, and it takes a while for people to get their footing on where they stand on a personal and societal level.
Add to that, school tends to breed that dominant/submissive pecking order in guys and girls during that age. Or are you guys forgetting the stereotypical "jocks" at your high-school. The macho idiots who pick on anyone and everyone to inflate their own sense of self-grandeur and salve their insecurities?
Anime is escapism at it's purest. It presents an idealised society and representation of both men and women so
of course they're going to be 'better people'! The only reason the idealised part is more apparent in the representation of women is that the anime and manga industry is heavily male-dominated, and therefore displays men's idealised portrayals of women.
/Rant.