MMA in Japan vs. MMA everywhere else in the world is viewed totally different. I'll point them out here and you'll see why the UFC doesn't run events in Japan on the regular.
-In Japan, MMA was treated as a spectacle more than a than an actual sport. Professional wrestling was treated more as an actual sport than MMA was. That's why you saw all the professional wrestling like "storylines" for certain fighters[Rampage was a bum living in a van on the streets of Japan who they'd drag out and have fight for example]. Even the production value of Pride FC was more along the lines of professional wrestling ala WWE than traditional sport. Big opening ceremony, fighter introduction, even Lenne Hardt with her over the top fighter introductions are a stark contrast to the "normal" Bruce Buffer introduction.
-Combat sports events are heavily influenced by the Yakuza. If you want to run anything combat sports related in Japan, you have to deal with the Yakuza, because a lot of the stadiums, arenas, and halls in Japan are in some way involved with the Yakuza on some level. Even the famed Kouraken Hall has Yakuza ties.
-Japan has no athletic commissions that govern combat sports at all. So the UFC has to bring their own people, who will do their own testing, and that costs extra money to put on a show along with doing independent testing.
-It's very hard for MMA to get on TV in Japan due to the fallout with Pride FC and the TV stations over there in Japan. A lot of stations lost a lot of money when Pride FC and its parent company DREAMSTAGE were outed as a Yakuza front. So MMA isn't a "Safe bet" in Japan like it is in many parts of the world, even markets that the UFC is just now getting into.
-Lack of Japanese fighters that are doing well. In Pride FC days, even though there weren't many Japanese fighters at the top of the ladder, you still had guys like Sakuraba, Gomi, Kid Yamamoto, and Shinya Aoki putting on competitive fights. Now, MMA has evolved to a point where it is extremely unlikely for a Japanese fighter to be competitive against an American counterpart. Japanese fans do not want to see Japanese fighters get constantly destroyed by American fighters.