When you have started as an independent dojo and begin to look at affiliation, the following questions need to be addressed:
1. What are the organization fees?
2. Are my students required to pay a membership in addition to the dojo?
3. What is the organizational philosophy of the organization?
4. What is their level of commitment to member dojos?
5. Who is the head of the organization and how did they get there?
6. Does their style of practice relate comfortably to mine?
There are many other questions you may wan to consider. Primarily, what are you looking for from affiliation?
Some organizations have fees for everything and you are expected to meet them. For example, you have your annual dojo fees, individual membership fees, and, testing fees. Find out what they are and what the expectations are surrounding them.
The organization's organizational philosophy is also important to know. How do they view themselves? For some orgnaizations absolute loyalty is everything. Others only want your fees and could care less what it is you are teaching.
The head of most of the preodominent Aikido organizations either inherited their position, rose to it, or held high rank in another Aikido organization prior to establishing their own. Just because someone started their own organization does not mean they know anything, nor, does it mean that they do not know anything. Research and ask questions.
Finally, does their style of practice relate to yours? This may require your attendance at several different organizations seminars and camps, or visits to their dojos, so that you can see for yourself just how they train. This is as important as anything else.
Then there is always the question as to why you want to affiliate at all.
Good luck in your search.
Yours In Aiki,