In a perfect world I'd ban Rinnegan entirely, Sharingan beyond it's first few levels, Senjutsu I don't think anyone lower than jounin should be capable really using it ever. The Uchihas just without their OPSharingan would be fine I suppose, whereas the Senju's I'd keep around, but not nearly as important, like they'd only have Yamanaka or Inuzuka level influence by the time of Chunin Exam Arc.

Perhaps as a compromise the Senjus and Uchihas are around but without their game breaking high-level jutsus they aren't nearly as important. Bijuu should be around but should be treated like WMDs. Making a Jinchuriki intentionally is akin to the Manhattan Project almost, and needs someone of Kage level skill to even ATTEMPT to pull off. Perhaps make the One through Four Tail capable of capture but difficult. Whereas Five through Nine are insanely difficult and the human cost to capture it is exorbitent. Remember the loose Nine-Tails crippled Konoha, with the Fourth Hokage, Sarutobi, Root, Kakashi, All the ANBU and Jounin in town along with the Toads and other summons. It's the equivalent of the North Korean Navy trying to capture a US Navy Carrier Group. You can try, but even with a positive outcome, was it really worth the cost? That's not even including the human element to keeping a Jinchuriki, it seems that most villages either treat them as a pariah, or a weapon, rather than a person. You really want a walking nuclear explosion that has an axe to grind against you specifically?