It has been argued that the Shintoism of Japan is made up of a big tradition and many little traditions. It might be more accurate however to state that Shintoism, or at least the major Shinto tradition which involves the imperial line is a construct which has been used to supersede the original religions of Japan. Japan is after all a fairly large place with many traditions which while similar can also be as drastically different from one region to the next as the Irish are to the Welsh, or the Cornish, or the people of Brittney. In other words Japan has or at least had a different religious tradition for each of its localities. Then during the Seventh through the Eighth Centuries the Imperial Court wrote a new text which introduced the idea of heavenly Kami to Japan, Kami who's goal it was to bring order to the Japan's existing kami and belief system.
In "A New History of Shinto," Teeuwen and Breen discuss extensively how what is now considered to be the primary tradition of Shintoism was constructed from Buddhism and Chinese belief systems in order to provide more power and support to the imperial Court. Even today the largest Shinto organization seems to be focused on this goal. This is not to say that the original faiths of Japan don't exist within Shintoism. These belief systems are very resilient and have adapted to this larger system with varying degrees of effectiveness. Rather this is to say that it is Japan's small traditions which make up its original faith. These small traditions are what exist within the folktales and folklore of Japan. In the tales of Bears which become the guardian kami of a village (http://zeluna.net/japanese-fairy-tales-bearspirit.html).
There are two sets of belief systems which merged in Pre-Shinto Japan, those of the Ainu and Emishi peoples who lived in Japan for thousands of years before the coming of the Altaic peoples from Korea who make up about 60% of Japan's Genetic makeup and who's language dominates the country. It seems likely, especially in studying the fairy tales of the Ainu that there was some amount of similarity between these two peoples. There are some Ainu fairy tales which can be used to better understand the original faith of these peoples. In addition I would recommend studying the works of Kunio Yanagita, the founder of Japanese folklore studies.
Many of these tales paint a very different picture of Kami then that depicted by the big tradition of Shintoism. It is interesting to note however that while the primary political movements of Europe attempted to demonify the traditions of the people Shintoism attempted to purify them, to remove their rough edges. To me though these rough edges are what makes folkloric research so interesting so worthwhile. Because Court religions, the belief systems of nobles were so sterile, they didn't deal with the scary realities of the ordinary person the way they needed to be dealt with. This is why small traditions persisted all over the world and especially in Japan for so long.