Imo Reptile's issue is that all of his neutral tools are just average, or worse than average. F4 lacks in range, F2 is cool but a lot of characters have 9-11 frame mids that advance, his jump ins are lacking, his anti airs are decent but not the best, his zoning is good but not the best, he doesn't have a dominant D4 like a lot of characters do.
When I play Reptile I feel like I have to get really risky with a dash, or just block, to get the first hit, for example.
As far as his damage, 50/50s, safety, etc, go, just look at the rest of the cast. Reptile is not in that bad of a spot. The best characters, like Mileena, Alien and Takeda, are all very dominant in the neutral. Reptile is not, for the most part.
Just my 2 cents.