In fact, VS projectiles have very diverse use cases.
With Lilith, you gain pressure, with Lei Lei you get imblockables, with Sasquatch you counter zone, with Demitri you zone, with Jedah you restrict the opponent, with Bulleta you AA... what you can't do is chip the opponent to death from afar through spamming bullets.
I really think having projectiles in Injustice is good, because it really matches the characters' powers ; right now, projectiles are useful without being too strong. While it can be frustrating, it's much better than having OP projectiles that make the game a bad Windjammers clone (best game ever BTW).