To my knowledge, this was suggested countless of times but turned down, however, not in this form to my knowledge.
More like an alliance of sorts but here it goes:
The option to "add under clan/village domain", you write the name of the clan, the founder/leader gets a system message or something like that and can accept or deny. Many of the clans reside in an actual village like TUC, it is listet in out "Konoha clans". Now, the added will be as part of the village clan in certain ways: Can use the halls as can the others theirs, may receive mass mails from the 30 and 31 of the parent/village clan.
Now, I know we already have villages and what nots but our kages and second in command can't edit the description, motd, or send mass mails to all of the villagers.
Another thing I wanted to suggest but left at the end as not as important due to the complexity it might hold, was giving the clan village the clan members of the clans under their domain w/o influencing their clan/rank membership. This would also allow the following:
X is a Tokubetsu Jounin to Konohagakure no sato and a 3 tomoe sharingan user to the Uchiha clan.
(somewhat of a combination between making village clans more village like and clan alliances)