The highest selling Monster Hunter has sold more than the highest-selling FF.
Best selling games ever in Japan, rank 11-30 :
11 Dragon Quest IX NDS Square-Enix 4,14 millions
12 Dragon Quest VII Play Enix 3,89 millions
13 Super Mario Bros. 3 NES Nintendo 3,84 millions
14 Super Mario Kart SNES Nintendo 3,82 millions
15 Brain Training NDS Nintendo 3,80 millions
16 Dragon Quest III NES Enix 3,77 millions
17 Monster Hunter Freedom Unite PSP Capcom 3,70 millions
18 Dragon Quest VIII PS2 Square-Enix 3,68 millions
19 Wii Sports Wii Nintendo 3,61 millions
20 Mario Kart DS NDS Nintendo 3,59 millions
21 Pokémon Heart Gold & Soul Silver NDS Poké. Comp. 3,58 millions
22 Wii Fit Wii Nintendo 3,56 millions
23 Super Mario World SNES Nintendo 3,55 millions
24 Final Fantasy VIII Play Squaresoft 3,51 millions
25 Final Fantasy VII Play Squaresoft 3,28 millions
26 Dragon Quest VI SNES Enix 3,08 millions
27 Dragon Quest IV NES Enix 3,04 millions
28 New Super Mario Bros. Wii Wii Nintendo 3,01 millions
29 Donkey Kong Country SNES Nintendo 3,00 millions
30 Pokémon Rouge Feu & Vert Feuille GBA Poké. Comp. 2,99 millions
http://www.nintendojofr.com/redaction/editoriaux/?id=aVzg
But is it a good metric to decide what franchise is the biggest ?