You're probably thinking, "This is a no-brainer. This kid ought to go with the closer dojo with the highly respected sensei (and awesome skill)."
I'm actually thinking nothing of the sort. Organizations don't really mean that much, the way kihon waza looks doesn't even mean that much necessarily, what is important is the quality of practice. How you determine that is another question. And if your dojo is still part of an organization then presumably what your sensei is doing is ok with that organization. Has no one ever tested for shodan from your dojo before?
I really can't say one way or another from what you wrote, I think you should think very carefully about which dojo you want to continue in. Sorry to be of so little help...