Think about it: Clannad basically flies directly in the face of the ‘good’ harem genre rules as originally set out in both Kanon and Air.
In this case, the standard rule would be: guy helps cute girl. Repeat as necessary (preferably a minimum of three times). This is what we saw in Air and Kanon, two shows adapted from Key games and considered to be examples of what harem could be if it had a heart and depth(ish) – both Yukito and Yuusuke bounce around like dangos helping the damsels in distress of their respective shows.
However, while on a surface glance, the same occurs in Clannad, there is something greater at work here – the girls are helping the guys more than the guys are helping them, as evidenced by both Tomoya and Sunohara’s transformations from when we first met them until the end (I am postulating from the Clannad game here in Sunohara’s case). Both Tomoya and Sunohara are introduced to us as delinquents of sorts, guys who are far from stellar academically, and whom just seem to overall not really care about where they are going in their lives.
But then Tomoya meets Nagisa, and finds himself, oddly enough, helping her in her quest to re-establish the drama club at their school. Tomoya doesn’t seem to really understand why he’s helping her, but he continues to do so nonetheless, and it is through this new interest in others that he ends up aiding Kotomi, Fuuko, and Tomoyo. However, even though Tomoya is helping these young ladies, what separates his actions from those of Yuusuke in Kanon is that Tomoya is playing a supporting role, especially in Tomoyo and Fuuko’s cases, while Yuusuke really took the reins in Kanon, and just seemed a lot more paternalistic overall. Fuuko and Tomoyo have already taken their own fate into their hands by the time Tomoya lends a hand, and they remain in control throughout (Kotomi’s case is a little more complicated, but she also hewed more closely to the standard visual novel girl overall given her past friendship with Tomoya).
Although all these encounters with the ladies of Clannad bring Tomoya further out of his self-imposed delinquent shell and out into the world, though, it is ultimately Nagisa who does the most to help Tomoya rediscover what it is to truly live. Tomoya slowly falls in love with Nagisa, and finds himself truly caring for something for the first time in ages. Yes, Tomoya helped Nagisa to her end goal of putting on a play, but Nagisa helped Tomoya become human once again.
Sunohara is a bit more of a difficult case to argue, especially as he still is pretty much comic relief in the anime in this point. At the same time, though, he is easier to make a case for, as he has done very little to help anyone thus far, outside of token aid to the drama club (and even that case was for selfish reasons). But who is the most determined to help Sunohara? Mei. And, in the game, it is ultimately Mei who does the most to help her older brother out, seeking the brother that she used to know who actually cared about what happened and about his own future. And since the second TV series is supposed to follow the game fairly faithfully, and is currently going through the Sunohara/Mei arc, I would say its a safe bet that it will similarly occur in the anime as such.
It isn’t altogether too surprising that Key would deviate from the previous formula at least somewhat on their third dating sim. Also, with family as the central theme, using female characters (traditionally seen in a sense as gatekeepers of the family) in helping roles makes sense. We could also further this argument of female characters as helping male characters by considering the role Ushio plays in the ‘good’ ending of the game – Ushio, in order to save her family, becomes the girl in the empty world and uses the garbage doll she’s made (which houses Tomoya’s soul, at least as I understood it) to collect happiness to save the entire family. Although the garbage doll, a.k.a. Tomoya, is the one who collects the happiness, without Ushio there never would have been any opportunity to do so, as she agreed to enter the world and is the one who gave Tomoya form in that world. All of which means that Clannad is further along in concepts of equality than Kanon or Air was.
Now please, please don’t kill Nagisa.