First of all, if there are many, many characters, there are probably too many. The more characters there are, the less we will be able to learn about them. They will just become dolls with different wigs on. So my first advice would be to decide between peripheral characters (of which you don’t need to learn much) and central characters, which you want the player to learn about in depth.
Chances are that by now you have a lot of central characters, so now it is time to delete and combine. There simply won’t be time for the MC to learn about a lot of people, because you, the author, has to sit and write all these scenes, and make them fit fluently into the story. If you have 100 000 words of character interaction, 4 main characters gets 25 000 each, but 10 only gets 10 000. So if you want to go deep, then you can’t go wide.
As for making the characters stay distinct… if they are too similar, why have two of them? That’s just a waste of space.