If you removed first party IPs and franchises that are not born in video-games (like Dragon Ball or Gundam), you get (in bold are those that has Smash representation, of any type):
1) Final Fantasy
2) Sonic the Hedgehog
3) Resident Evil
4) Dragon Quest
5) Monster Hunter
6) Metal Gear
7) Tekken
8) Street Fighter
9) Pac-Man
10) Mega Man
11) Kingdom Hearts
12) Souls
13) Power Pros
14) Devil May Cry
15) Castlevania
16) Frogger
17) Simple
18) Tales
19) Megami Tensei (includes Persona)
20) Professor Layton
Its great that the top 10 best selling Japanese IPs are in Smash, and 7 of them with playable fighters. Its interesting to note that in the first 3 games (Brawl, 4 and 4 DLC) they go for the biggest names (Sonic and Snake in Brawl, Megaman and Pacman in 4, Ryu and Cloud in 4 DLC), then in Ultimate they decided to start exploring IPs that are a bit less successful in sales (although in base game we got Monster Hunter, as an AT sure but I think that was an internal decision with thinking about the best way to represent that IP, if they want, they could have add MH as a fighter). I hope that in this FP2 they will concentrate in top 11-20 with more representation like Kingdom Hearts (that is likely it will get in top 10 very soon) and Devil May Cry. I think that Dark Souls can work as a boss just like Monster Hunter, rather than a fighter.