If clans do get their own jutsu I could only tolerate clans with extra abilities being made if they are not to access for example, forbidden jutsu. I wouldn't want to be at disadvantage just because I am not in a clan.
Also, there's nothing really wrong like you try to point out with the current ones. The large clans that were made example Kuraen, Hozuki, Mirana, Sasayaki all function and were large/semi- sized groups that became more than just an ingame clan. Some even already have their own uniforms.
So in my opinion forcing players to only choose from selected few clans instead of creating their own, limits the possibilities of imagination and rp and simply amassing a horde of players into few clans isnt really good idea.
Also Name-changes do not affect gameplay in anyway since the game is rp/pvp, again taking out the freedom and possibilities just to make some ban-tracking job easier... Joining a clan will never feel permanent if you dont commune with other members and just do it for the name change or for some "ability"... sigh
PS. Game already feels limited because of certain "rules", don't make it less so. Also I am in no way trying to disrespect or bad mouth the ideas set by the development team and am simply stating my honest opinion on the case.