What it comes down to.
Yes, his hitbox has issues. No, it is not any worse than any of the females + Scorpion and maybe even Bo Rai Cho.
Once that is out of the way, why are we banning him? Because he's a good character? Does everyone agree that he's in a tier of his own and easily the best, by far? If not, I don't see the point. In my opinion Piercing Mileena, A List Cage, Cutthroat Kano, are all better than any variation of Alien. There are others that agree that he's not top 1, who don't even play the character. If the character is just a consensus top 5 and thought to be top 1 by some, then why should he be banned?
We need to stop with the "downplaying" and "you just play the character" rebuttals. If you don't have any legit points to back those claims up, then they're meaningless. Tell me why i'm downplaying, tell me why i'm being biased. If you can't, then those statements hold no weight.
Lets look at the reality of the Jax MU. Jax can't use his B2 which is now full combo punishable, so why can't he just use downward superman? It's faster, grants a full meterless combo in the corner, needs a bar to combo midscreen. Why does he need B2? If B2 didn't exist Jax would be the same character. Also, lets not forget that Jax can rival Alien's neutral and he can full combo punish regular flip. There's no way this match up is in Alien's favor. Alien probably loses.
I'm giving the Alien upplayers more than they deserve with the above paragraph. In reality the best way to get around Jax's B2 with Alien, is by blocking it and punishing. You'd have to be a complete idiot, if you were to attempt to make it whiff in a real match. Why not just block it and get a full combo? I was messing around in practice mode and I would often get bopped by it. Worthless bug imo. Much less useful than ducking a Shaolin Kung Jin upkick with a female hitbox, or using a female vs Sub Zero. Mileena is as good as Alien and can make Jin's upkick whiff, if he does certain strings into it, that Jin's do use. Why is she not being banned? That's very relevant in that MU. Jax's B2 whiffing is not.