Yeah, one of the biggest disappointment on 3DS (with DQM J3 and Yokai Watch 3).KH3D's performance is still a bit of a mystery to me. The game is a bit rougher than BBS but not to the extent that explains the massive gap in sales and it's relatively important to the series on going plot too.
Not only it performed significantly worse than BBS it also performed well below 358/2 Days on DS and KH3D was released when 3DS was booming in Japan!