Reptile's variations are fine.
Look, you're missing the forest for the trees, here.
Has it occurred to anyone, anyone at all, that because of the core design of Reptile, that he doesn't need a bunch of fancy variations? That all he might need are a simple, passive buff, the ability to go FULL invisible for FREE, and a way to extend his combos?
If you are of the school of thought that he is a copy/paste from MK9(and I don't necessarily think this is 100% true), then you know that the following things were true:
Reptile's zoning was good. Not great, not amazing, not Kenshi or Freddy, but good. Solid.
Reptile's pressure was good. Not great, not amazing, not Sonya or Johnny Cage, but good. Solid.
So already, you have a character that can do a little bit of everything. Maybe not as well as the guys that specialize in either or, but he has tools for different situations. So if your base character already has these tools, why would you fuck around with the design with a bunch of unnecessary, elaborate, gimmicky stuff?
You have his Deceptive variation. I wrote a pile of stuff about this in UsedForGlue's other thread. Go read it. I really don't want to re-write it, here.
You have his Noxious variation. Does anyone here remember how god damn annoying/heart-breaking it was to fight a Black Adam player to a very close life situation, only to have him fucking walk at you and kill you? Or Black Adams that got a big lead, walked back, and threw shit at you, knowing that when you tried to hit them you would take damage? The same applies here, only it NEVER GOES AWAY, AND YOU CAN BUFF IT TO DO MORE DAMAGE. Why on earth is that considered bad? That's fucking good. You don't NEED to be constantly in that ass like someone in this lame thread already said. You go in. You get a decent lead. You back off and do some zoning and make them come to you. Then you punish their approach attempt with a downpoke, or elbow dash, or anti-air, or something like that. Even if they DO get in, you are dealing damage to them while blocking.
You are doing damage to them while you're BLOCKING. Do you realize that this essentially makes Reptile amazing at winning The Clutch moment? On top of that, you still take damage while you're hitting him. You could be doing the game-winning combo when his enhanced chip just fucking kills you. Just fucking kills you, like that. Wow. What a nightmare. I would hate having to deal with that. Did I mention that the base version is free, and never goes away? It's free, and never goes away. Holy hell.
You have his nimble variation. Can we talk about how absolutely terrifying this variation could be? The Flash never had projectiles. He especially never had projectiles that went across the screen at different speeds, and could be enhanced to go faster/slower, and could be stopped at any point on their travel. Now imagine all of that, but you now slow down time. You MIGHT(notice the word choice) start a combo, go into Nimble, put out an enhanced Fast ball, continue your combo and have them LAND on your fast ball by the time the nimble is finished. This is only a hypothetical. I don't know that it's true. Even if you can't do that, do you realize how amazing your screen control could be if you could put out a slowball, go Nimble, and then just react to whatever they try to do? Try to jump? Get anti-aired. Stand and block? Thanks bro, I'm going to run in and start pressure. Oh, by the way? My slowball is still behind me and when this slow-mo bullshit is over, you're still going to have to deal with that. What if, with proper spacing, you could use Reptile's throw while in nimble to throw people ONTO your forceball? How awesome does that sound?
The TL;DR version: Reptile's variations aren't meant to be three different dudes. They're meant to enhance the shit he's already good at and compliment his existing tools. I don't have to re-learn my character three god damn times? Fucking right.
How on earth could that even remotely be considered bad?