After a long search, my son finally found a very good Karate school ( http://www.kyokukai.com/ ). The teachers and students are all very skilled, down to earth and very friendly. They are also very foreigner friendly. The school concentrates on "Karate Sabaki Style" (self defense and full contact) and is a mixture of traditional and modern karate. They also allow grabbing, throwing and grappling to be mixed with punching and kicks making it a complete art, plus they also teach weaponry.
New students coming from other arts (like my son who came from Judo-CQC-Arnis-Kali) will find the school very open and welcoming. The school is not rigid to their own style alone and will develop their art with the old art that the student has, making it an explosive-hybrid combination of skills and techniques.
The blog below was our school's BBQ last Sunday. The sun was good, food was great and we had lots of fun. I also have joined the school as CQC-Arnis-Kali instructor. If you are searching for a fun and no BS Karate school in Kyoto Japan, please drop by and share the fun :)