Super Smash Bros.: Snake, Ryu
The former because he doesn't fit with the rest of the cast at all, the latter because he is already the most iconic character in another fighting game series. Merging franchises just for the sake of it is distasteful.
Halo: Miranda Keyes
She could have been an interesting addition to the very small cast following the original title, but the developers wouldn't allow her to become more than a boring female token.
Mario Kart: Baby characters, Metal characters, Koopalings
Just because the game is new that doesn't mean you have to add tons of characters to the roster. Less is more in this instance.