I've been playing some of the 3DS BiS, and there are less contentious changes than in the prior remake. It's obvious that it would have disappointing sales even if it was an excellent all-new game, though a bit less so. So I'm not sure if it's fair to say that the series should be scrapped because of boring games while also holding up BiS as the best, which Alphadream seems to acknowledge (Plus the linear, minigame-centric DNA of the later games was sort of set by BiS, not that it can't be done well.)
It would be nice to see their animation skills applied to other things as well, of course. But I'm not sure what bankable Nintendo properties are as suited to their style as Mario. Until we hear a definite, the prognostication that either Mario spinoff series will be discontinued remains wishful(?) thinking among the diehard fans.