I think he was seen as more dangerous and boring than anything else. Kind of like Jon Fitch. Only Okami was brought in specifically to fight Anderson.
I don't agree with the cut, but that is the only reason I see. He beat Lombard, who was very marketable. He beat Belcher, who might have been marketable, and both performances weren't barn burners by any stretch of the imagination.
If you think about his last three fights, he was brought in to lose. Belcher had beaten Paul Harris and was getting serious hype, he was suppose to beat Okami in a sort of revenge/redemption match. Not to mention, a win over Okami would have put him on a five fight winning streak.
Lombard lost a controversial split decision to Tim Boetsch. Then he beat Paul Harris, and Yushin was on a two fight winning streak. If he had won it wouldn't have been hard for the UFC to promote him into a title shot.
It could be argued that all of Yushin's fights since his title fight up to Souza could have been for him to lose. The only questionable guys in that six fight span are Boetsch and Roberts. Roberts was a late replacement, though I don't think he was brought in to lose against his initial opponent in Luiz Cane.
Boetsch had a small amount of hype, going into the fight. So you can't really tell if Yushin was supposed to lose. It seems like it, a lot was talked about how strong Boetsch was. So the brass might have thought Boetsch could be a name off Okami, who they really had nothing to do with at that point.
I could be wrong, but this is the only justification I can give.