In Japan I think there is a reasonable argument that the series is at best the ninth most important series of the generation, rather than top three as in the PS1 - PS2 eras, as eight series have topped 3m in Japan on the machines released after 2004, and Final Fantasy isn't one of them (and I think stuff like Smash Bros, Nintendogs, and Mario Party is arguably above it too now actually). So in that sense, yeah. Japan has seen far better days for the importance of Final Fantasy.
If you look back in Japan you generally have 2 - 4 series capable of 3m plus entires until very recently when more random types of games began to sell well.
NES: 2D Mario, Dragon Quest
SNES: Mario Kart, 2D Mario, Dragon Quest, DKC (Street Fighter and FF are close, but not quite at the level)
GB / GBC: Tetris (late NES era), 2D Mario (late NES / early SNES era), Pokemon (PS1 era)
PS1: Dragon Quest, Final Fantasy
PS2 / GBA : Dragon Quest, Final Fantasy, Pokemon
DS / Wii / PSP / PS3 era: Brain Training, Wii line, Animal Crossing, Pokemon, Friend Collection, 2D Mario, Mario Kart, Dragon Quest, Monster Hunter
So in terms of big hits, the diversity of recent years seems to have knocked Final Fantasy back to where it was in the NES days, as a big (1-3m) but not huge franchise. You essentially have three RPG brands in Pokemon, MH, and DQ, and five casual brands in Brain Training, Wii-line, Animal Crossing, Mario Kart, Brain Training.
Essentially there were four break-out hits this generation - Monster Hunter, Brain Training, Friend Collection, and the Wii line (Wii Sports, Wii Fit, etc) with the rest (DQ, 2D Mario, Mario Kart, Pokemon) continuations of old brands.
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