There are a lot of past threads on the subject both here and on AikidoJournal. The latter has a great series of articles on Ueshiba and those most intimately connected with him. I would suggest you go there before you speak further.
Summarizing (and this includes paraphrasing by high ranking Aikikai folks on the lists and Aikikai shihans to me directly.
There was a change in emphasis of Ueshiba M after the war when he was already an old man. None of the uchideshi, especially the pre-war ones, were particularily interested in Ueshiba M.s religion and the master himself did not make his religion a requirement to study Aikido. His son, Ueshiba K. and other of the post war students took Aikido in a direction different than it was before.
As Stanley Pranin says in his Artilce on Tomiki - he rooted his Aikido firmly in historical Budo. There is no travesty to say that Shodokan (Tomiki) Aikido is not Aikikai (Ueshiba) Aikido. The latter went in a different direction - although the root is the same.
We have bowing to Shomen and sensei at the beginning and end of class, there (at least in Honbu) is a bow to begin and finish training with a particular partner. In addition there is a loud verbal please and thankyou with each bow to a person. These actions (with some variation) are common to most gendai budos in Japan. There is no heavy shintoistic clapping. At the class of the Osaka Aikikai Shihan I think he clapped once. In Okinawan Karate there was no bowing at all, and the one time I trained at a Koryu dojo we just bowed ourselves into the dojo and started training. Ettiquette was buying a round of beer afterward.
When I refer to anal I refer to what I saw - I have no idea how you practice. I have been lectured on how the Japanese behave by people who knew that I had lived, worked and trained there for almost six years with "ettiquete" which I found way over the top.