[quote=Origin]
Okay I'm pretty well versed in Naruto in my own opinion but on the subject of jinchuriki I have a few questions since i've never been able to grasp what stops them from being in perfect control....So the bijuu is sealed in the persons body but how does it work? Is the bijuu held in the body or in the seal?If he is held in the body then you wouldn't need permission to access it's chakra because you are the one in control of your body. It's soul may have had a link to the chakra before but that connection would be severed as soon as the chakra was now in your body (Ya feel?)However from the looks of it the bijuu is held in the seal, ultimately with control over the seal you should have control over the bijuu in my opinion, it should be easy to make the bijuu submit to you since you can control the seal and make it's life hell. If we take the case of Naruto the nine tails dwelled in his mind if I'm not mistaken which is HIS mind so he should be able to set any variable for it that he wants. Inflict pain and make it loyal to him.. if it can't feel emotions he can make it because in his mind, he is god.There leads to my question why do we not have every jinchuriki in full control over their biju?
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It's sealed and restricted inside.
Though you can assume that each village uses a different sealing method. Thus circumstances are different all around. We only really got to see the aspect surrounding Naruto's seal upon the fox, but that was a very specific sealing with specific circumstances. But, the sealing method would have to be strong enough that the Bijuu couldn't just take complete control of the Jinchuriki from the start. It took a lot of anger and pain for Naruto and Gaara to have their Bijuu start to take over. Though I don't believe you can have control over the Bijuu as it is sealed. Naruto released his to access the full power of the fox then had to subjugate the fox. The Jinchuriki could be taken over upon the release of the tailed beast so it would require a strong Jinchuriki to get to that point in which they can utilize the Bijuu's power. 

Also, consider that the Bijuu is no weak thing. Even if it was in Naruto's own mind it could fight back. It was also protected and surrounded by the seal (the cage) for a long time, thus beyond Naruto's manipulation until the seal was broken, in which the Fox could fight to take over Naruto freely. Realize that if Kushina did not appear and aid Naruto in subjugating the fox, Naruto would have been taken over.