Personally, I feel it's a combination of problems. One, the 3DS is still relatively new, and it's somewhat underwhelming current library means not everyone has one. Second, MoF tried to be an HD Home Console quality game, on a handheld one. It was made in HD and "scaled down" third, it tried too hard to pander to the people who complained about the first one. As a result, it feels... strange. there were some strange gameplay and design choices. (collectible monster bios for one...)
Also, it just feels disjointed due to the reverse story. it should have been a console game, and it would most likely have been a completely different game, most likely more like LoS1, meaning no 2D gameplay. And that probably would have been for the better, since LoS' gameplay doesn't quite translate well to 2D. It was really kind of forced.
As far as "no more handheld CV's" Im honestly not too bothered by that prospect. Castlevania has been relegated to Handhelds for around a decade. With console attempts usually falling short or just failing.
Now that we've had a successful Console game... And an unsuccessful handheld, maybe it will give Konami the impression that they need to shoot for more console games with Castlevania as opposed to handheld. And that's probably what the franchise needs. To finally re-establish itself as a console series, not just portable handheld adventures.