I belong to a federation that is not affiliated to the Aikikai. It's not something that normally enters my consciousness.
I practice with a teacher who has learnt from a number of O'Sensei's direct students, as far as I'm concerned, the quality of your teacher and his/her teaching is far more important than the name of the organisation or the 'validity' that is given or not by a 'governing body'.
I have no negative thoughts regarding any other aikido 'group' as long as they uphold the spirit of O'Sensei's teaching.

regards,
Mark