You're not wrong and I never specifically said that Supergirl/Powergirl could never make the cut. Rather, I simply pointed out that between a character that plays similarly to another versus one that plays radically differently (in a balance-able but interesting way, obviously), the latter should be the preferred choice for the sake of gameplay and game mechanics.
Also, with MvC3, one must bear in mind the number of characters in the game. In MvC3, there were 36 (+2) characters (with a further 12 more in the updated version); for a total of 50 playable characters (48 if you exclude DLC characters). While there isn't an official number of playable characters in Injustice as far as I'm aware, the character selection screen layout as shown in this picture
suggests the figure will be somewhere around 24. That's half the number of characters in UMvC3
(2/3 compared to MvC3 vanilla)!
The implication of that is simple: From a gameplay perspective, MvC3's characters do not need to be as unique from one another as Injustice and that the former could get away with smaller differences between characters simply because there are more of them to fill out the various niches. Meaning, while it may be fine for there to only be a small distinction between Hulk and She-Hulk or X-23 and Wolverine in MvC3, the same principle may not necessarily hold true for Injustice's characters and character design.