1.... I could still learn a great deal from him.
2...I seriously wonder if our dojo's brand/style/flavor of aikido is congruent to the national org. and hombu.
3...another dojo in the same org that is actually a little closer to my home. This dojo has a very respected sensei in the national org. with truly awesome skill...their "flavor" of aikido is also very congruent with my own personal taste.
4...sense of loyalty to my sensei.
Hi anonymous. A difficult situation but you have to tease away the main points.
FIRSTLY and most importantly - only YOU are ultimately responsible for your aikido progression. If your goal is to become a great aikidoka you must train at the club which you feel will teach you the most at this time. This does not necessarily mean you won't train at the other club later; but think for you, at this moment, what you need fo progression.
Point (2) is irrelevant. It does not matter what affiliation or organisation you belong to. If you want something more popularist, why not take up karate? The point is, you have to decide for yourself which is best. Also in point (3) - just because someone is respected by lots of people does not mean they are great (vis. Adolf Hitler) and just because someone is not respected does not mean they are crap (vis. Jesus). Make your own decision.
Point (4) - yes, I understand this sense of loyalty to your sensei, but sensei's are still students of aikido. Train with who you feel you have most to learn from (or train with both if you want). It seems however that it is your sense of loyalty which is keeping you there. If your sensei is humble and modest he will let you do what is best for you. You never know, maybe you will re-enter the dojo in a few years with more wisdom?
Good luck in your decisions!