What you said about giving either male or female characters, depending on the target audience of the series, various color schemes, designs, and personalities, is very interesting. In most of the harem anime I’ve seen, the one main male character is fairly cliche and uninteresting, while the females have distinct looks and attributes. And in most male harem series, the male characters are diverse and attractive, while the female protagonist is an unforgettable “Mary Sue.” There are plenty of exceptions of course, but that’s a good point.

There is one other factor besides target audience, however, that can very easily tell you whether an anime or manga is shonen or shojo – something called the “object of desire.” Which characters are displayed in a way that makes them most attractive to the opposite sex?

In shonen like Haruhi, the girls are given widely varying color schemes, personalities, and interesting costumes, so that male viewers can easily pick out their favorites based on their moé fetishes. On the other hand, the guys wear boring suits and both have short-ish brown hair. In Fushigi Yugi, it is the boys who are the objects of desire. They all have vastly different personalities, hair colors/lengths, costumes, and skills, so that girls can pick out their favorites based on their bishonen fetishes. The main character Miaka is nothing but a klutzy, forgettable “average girl.”