[quote=@GrandzHelios]
Are there any off limit ninja clans/abilities?
[/quote]

Not really, no, as long as you have a good explanation for them being there. Like, if you play an Uchiha, how did that Uchiha end up in Gobi and why. Simple like that.

At this point, a lot of the annihilated clans haven't been brutally murdered yet, clans like the Uchiha and Yuki are still thriving.