The more lovey dovey the serie is, the more NTR it attracts. I mean look at Oh my Goddess... we have already several artist doin awesomely long NTR series about it, its natural for these to be drawn
Edit: never said it has to be a "Great" series, just lovey-dovey and yeah sorta the main character being weak is part of the equation
Anohana is not lovey dovey and yet there's plenty of ntr, haganai has two girls fighting for the same character and the ratio totally favors harem/vanilla. I think it's an issue with the main male character, with how he looks or behaves.
Go take a look at Clannad, if you take Carn away there's almost nothing left.