It's not a matter of how many trophies there are this time, it's a matter of what trophies they put into the game. Generic items, duplicates, spam... 1 different trophy for each pikmin color, for example... why not simply a trophy for all the pikmins at once? and some series got lots of trophies specific to different games (skyward Sword, Twilight Princess, Windwaker) while others got nothing except some generic references and the main character.
The handheld games are not represented enough. No oracle trophies, no minish cap trophies, no Marioland 2 trophies, no any other retro handheld game is represented with some rare exceptions; only recent casual games like Kawashima and Nintendogs are represented as handheld.
Important characters from the history of Nintendo, such as the classic version of Ganon, are not represented, and never got represented in past Smash games as well, which is stupid.
anyway, I discovered something in my playthrough:
the alt. trophies for the characters are unlocked in the all stars mode as well, not only in the classic (I did the all stars with everyone first, and I got them in the shop).
There are a bunch of very expansive trophies that appear late in the shop. They cost 2500 (and I'm not sure, but I think there are some that cost 5000 as well... not sure though). I don't know when they appear, maybe they appear after buying all the alt. trophies, but again, I'm not sure (to mention some of them, the Game & Watch consoles trophies).
There are some trophies that are exclusive to Trophy Rush.
When you have around 610 trophies (more or less, depending on the challenges), you can't get any more trophies from most of the modes (assuming that you never used Trophy Rush like me). If you want the last trophies you need to play Trophy Rush, they can be obtained only in that way. Those trophies are mostly smash items.
I can make a list, since the last trophy I got was the prince of stable, everything above it is a Trophy Rush exclusive, or something got through challenges (I have to remove them). Maybe I'll do it later.