The problem with the FF1-3 and FF4+ compared with 2D vs 3D Mario is, 2D was Mario at his height. On the other hand, FF's popularity just kept rising after FF4.
I don't think the audience for FF1-3 is as big as the latter. Now, I don't necessarily think current Final Fantasies are as doing as well as they could be, but I think FF4-8 (and 10) is closer to what most people would prefer.
While the battle system of FFX was my favorite, it probably had too much focus on story (cutscenes). Some balance between this and all the older FF's could definitely make a great game that many can appreciate.
Eh, who knows what The Last Story could turn out like? Just wait for details!