You are somewhat right about the discrepancy here.
However, your system will ultimately cause balance of power problems. Let's say some clans become "Official" and choose their own unique abilities. This would make these official clans (which already must be much more powerful compared to the rest) even stronger. They will end up getting much more applicants than any other clan. Who would join a low-member clan with no special skills when they can join a populated one that has exclusive powers? Basically no one. My point is, these official clans will get both unique powers and more population. Other clans will get neither.
In my opinion, there should only be official clans and that is it. Meaning no clans with just one or two members. This game is only getting bigger and more famous. Think of how it will be around release. If anyone had the ability to make their own clan, it would be hectic. Having hundreds of clans with just one or two players.. it's simply unrealistic. It might not look like it now, but soon it will turn into chaos. I say have only official clans. To be a clan, you need at least eight players to write down their names and register for that clan. The fact that eight players wanted to join a clan means that that clan must be special enough to deserve a place in the world. Because frankly, there is a limit on that.
That way, there will ultimately be less clan numbers, and more clan members.
Now, about the special abilities. This suggestion can happen, but not in this period of time at all. In fact, maybe a little while before release. There could be some sort of clan competition, with two or three winners from each village. The winning clans get to choose a special ability that can be implemented. That way, people who applied for that clan would have joined not because the clan has special powers, but because it actually has nice history/ physical features, etc. So in the end, like you suggested, only a few clans per village will have special abilities. The rest will still be official clans but without any. However like I said earlier, these clans are special enough to have a place. Since they got the interests of eight people, they will still be able to get more members because of it's features.
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