I'm just starting to flesh out my Reptile, myself. I'm not an expert but what I've been doing is different for each opponent.
He's a great zoner but obviously Kabal is dangerous, Sub Zero with his insanely fast projectiles leads to unfavorable trades, and teleporters just suck. You can bait teleporters into punishers, which is where knowing some of his juggles can come in handy. But for the most part staying close, rushing in and making sure your runjabs are canceled with block is best bet. I'm still a newer Reptile so against high tier characters powered by competent players turns me into a blocker but I'm breaking out a bit. You need to be deceptive.
He seems to have a sweet spot for throwing forceballs where you can get away with letting one out while having enough recovery time to block counters. For his zoning it's a matter of feeling out those safe distances and knowing his recovery times. I've been able to get away with things I wouldn't have even tried a month ago because I was afraid risk wasn't worth payoff.
His slide is a good quick punisher when you're in a pinch (blocked high kicks or sweeps where distance is too great to run in for an autocombo). Fucking annoying online. Sliding to punish crossup jumps is effective, though I'm pretty terrible at executing on XBL.