Sub and Rep do suck compared to everybody else. Other than the roundhouse, they have the shittiest normals in the game. They also get raped up close by other character's jabs and there's very little they can do about it. So does Scorpion, but he has better mobility, better mixups, an air throw that can snatch other characters out of their special moves, easy high-damage combos, and can lock down blockers in cross-over traps that never seem to end. The only thing they really have going for them is their walk cycle and that roundhouse.
Sub isn't total garbage because he has high-damage options if he's willing to trade and Reptile isn't total garbage because he has the wildcard of invisibility. Both characters, however, have to play very wisely and not make any mistakes in order to succeed. Every fight using Reptile and most using Sub are uphill battles. They aren't helpless by any means, but they (and Baraka) are the bottom of the barrel in this game.