Yet when a character like Makoto Itou of School Days decides to act like a man and take advantage of the opportunities presented to him, everybody calls him a jerk/asshole/etc. I would agree with zherok's assessments that they are supposed to be blank slates for audience identification and self-assertion. The flip side of that is that if the producers want to move merchandise, they have to make the female characters dance a line between sexual attractiveness/willingness/availability and virginal demure pureness. Thus the need to make male leads overly passive/weak/scared, lest they create a Kannagi-esque "mai waifu has been defiled!!" situation. (And that was just from a backstory mention of the female lead having had an ex-boyfriend at some point in the past.) Other causes for indecisiveness include the challenges of adapting multi-route VNs or incomplete manga.
I would say that male harem leads fall into one of three molds:
1) The scared/weak/inexperienced/shy boy who is in some cases actually allergic to female contact. Examples include Love Hina, Girls Bravo, Hanaukyo Maid Team, Maburaho, Please Teacher, Onii-chan no koto, Sekirei, Omamori Himari, Vandread, and various others, often from the early/mid-00s.
2) The "indifferent/indecisive" lead who's either "above it all" or trying to eke out a normal life and normal relationships amidst all the crazy hijinks that surround him. Examples include Da Capo, Shuffle, Air, Kanon, Clannad, Happy Lesson, OniAi, DearS, Nyan Koi, and Please Twins -- these tend to come from the mid/late-00s.
3) The "aggressive/perverted" type who tends to be more traditionally masculine in stature and behavior. Most of them can't take things too far because of the constraints I mentioned above, but they are a bit better than the average. Examples include Yumeria, Goshuushou-sama Ninomiya-kun, High School DxD, Princess Lover, Nakaimo, School Days, and Aesthetica of a Rogue Hero -- becoming more common in the late 00s/early 10s. If these broad trends over time are any indication, maybe we will see an evolution away from the wussy types.
Gintama and Mushi-Uta definitely do not fit.
Then we have Black Lagoon with Rock in it, and it doesn't really fit either.
None of which are harem anime, which are the main subject of discussion here.
When it comes to watching harem anime, I accept that they are wish-fulfillment, and try to appreciate the looks, personalities, and behaviors of the female characters without directly trying to identify with the male lead.