Masaki, you're like a walking facepalm...

Character traits like Bijuu and Jinchuuriki as well as Mangekyou and Eternal Mangekyou as well as even Rinnegan aren't inherently bad traits, but as with the real continuum, they must be placed effectively. Look at those whom wield them. In this world, it was Sai, and he successfully - albeit temporarily - took over the world. Granted, he did that without using Mangekyou or Rinnegan. I limit them highly so that when you do actually see them, you understand the awe of the character. Shin, noted as the strongest living shinobi after the fall of Sai, doesn't even have Mangekyou. If someone gets it, it will be for a very, very valid reason.

Jinchuuriki are present, and you needn't worry about their power levels. The strength attained from a bijuu is dependent on the strength of the seal and the depth of the Bijuu-Jinchuuriki bond and relationship. No one is getting one because I will require a roleplayer for each bijuu, and not only do I not want to assign resources like that, I don't feel the roleplay has matured enough for it.

What I will note is that it is possible and that in this world there does exist the Mangekyou, Eternal Mangekyou and Rinnegan - all as possibilities. All as enigma. They are not of you or your characters' concerns at the moment. The same goes for Jinchuuriki, even if Konoha has three.