Well, right now I'm getting my way through ripping Inazuma Eleven, starting with some of the NPCs and (eventually) moving on to the actual playable characters. Just looking at the characters in general, it looks like the only things that differentiates one between the other are three things: the portrait, size, and head.
For the portrait, there are 6 different ones to chose from, depending on the size of the character. There are also 7 skin tones.
There are only 2 different sizes (overworld) that I have seen so far in regards to playable characters, one that has the torso at 16 pixels high and the other with 17 (the number adjacent to the portrait indicates what size their overworld is).
The only thing that changes between playable characters is the head (and the uniform of course, but each character can be in multiple uniforms, depending on what's happening in the game). When comparing multiple characters next to each other (in the same pose), the only difference between them is their head. Simply put, there is a base uniform that the head sprite goes onto, with it overlapping the uniform sometimes depending on the length of the hair, etc. (the skin tone also changes in the overworld sprites' hands).
As for how many characters there are, I can't really count how many unique sprites there are, I'm not one to say an exact number, but I'm guessing somewhere in the multiple hundreds. There are 13 teams with 16 players on each team, adding up to 208 characters, not including random players on the clubs around school, your team and the NPCs that you see randomly around the game. Just looking at the player list in the game, it looks like there are about 748 playable characters total.
Hopefully I helped explain it a bit, I kinda just kept rambling on. If there's anything I missed, I'll try to clarify with what I know.
EDIT: There are actually 8 different skin tones (one that I just noticed today), sorry.