Logically the only reason people still cling on to Cyborg Smoke is because he's from the Old Timeline and is a nostalgic character. That's it. Literally!

I've always been a fan of Smoke, and I particularly wanted to see what he was like as a human. I got to see that, and I'll get to see that aspect of the character explored further in future. Regardless if he turns into a cyborg, a demon, a demon-cyborg, a zombie or even Tyra Banks, I'm just happy Smoke's on the roster at all. He could have easily become tarred into Rain and Skarlet's DLC bandwagon and left with no limelight in the story at all.

MK9 has defined the character. He now has an origin, a name, a nationality, a personality, and a distinctive look. These were things we could only speculate about in the old days, wondering who Smoke was beneath the mask...now we know them as fact. It's the first time he's ever had his own entirely original moves list too, original fatalities and his own gameplay where he hasn't got recycled animations or attacks from other characters. Not becoming a cyborg was the best thing that ever happened to him. I honestly don't see what people miss about Cyborg Smoke in comparison to what we have now...an indigo robot with Scorpion's spear and Sektor's teleport who got locked in a dungeon, forgotten about by his best friend and then re-programmed years later to act as Noob Saibot's personal bitch is a really shitty character arc in all fairness.

I honestly think the Smoke episode of Defenders of the Realm was a better told story than Smoke's bio, ending, and appearances in Story Mode.

That's why I "cling" to Cyber-Smoke. Because I miss the emotion behind "I escaped and my friend didn't and I feel guilty about it and now we're forced to fight each other. Please dude, remember who you are."

I mean, there was certainly none of that between human Smoke and Cyber-Sub in MK9. Maybe I would've been alright with the role reversal if they'd actually had Smoke go through what Sub went through in MK3, but nope. Smoke gets to stand in the back while the Council of Elrond meets in a church, doing jack and shit until he dies, and Cyber-Sub is only evil/controlled for a single scene, opposite Kabal who's never met him before and thus has no reason to feel any kind of way about him.
For me, it's pretty much that simple. An episode of a shitty cartoon where Nightwolf was a computer nerd, they all flew jets, and characters had painfully bad catchphrases still managed to do something better than the game, and because of that shitty cartoon, I'll always believe Cyber-Smoke has more story than Human Smoke.
"More" in the sense of emotional content, rather than sheer information. Having a real name and birthplace now is nice and all...but those things retroactively apply to Cyber-Smoke too...and they don't actually make the character "deeper", the only thing about that biographical data that actually informs his personality is the fact that he has no family so he considers Sub-Zero his family...and that was already true, we always knew Sub was his only friend.
Hell, MK9 didn't even show any of the automations, while the shitty cartoon knew enough to have a scene of him screaming on the lab table. Where did the body horror aspect of being surgically altered into a fuckin' robot go, huh? MK9 is so goddamn shallow and emotionless, there's never any drama to anything except the death scenes.
I also think the Rain episode of that show gave Liu Kang and Kitana more personality than MK9 did, incidentally. I miss the whole Highlander-ish "now that I'm champion, all my friends are gonna age and I won't, I feel lonely" aspect of Liu's story.

But the cartoon only takes some aspects of the story that are canon, the rest isn't. Honestly if you're willing to compare a cartoon where grey robots can be knocked out with one punch and Jax is overtly emotional for a high ranking soldier to the portrayals in this game (however lacking some characters were), well then there's not much I can really say. If that's your personal tastes, fair enough.

Bear in mind, the rendition of Cyborg Smoke we're curious about is the one from the actual games, not the cartoon. Realistically, in the games his story never went anywhere. Yes, it had potential, but it died almost immediately by the time MK4 was out. Sub-Zero never bothered to try rescue his friend from his robotic form in all the years from Shao Kahn's invasion to the return of the Dragon King. The suffering Smoke went through becoming automated was almost meaningless, once the invasion was over Smoke just became a forgotten chapter in Sub-Zero's life, a dusty trophy locked up for years in a castle.

If it was my best friend who became a cyborg involuntarily, I wouldn't be like Sub-Zero and completely forget about him. Fair enough he had Sektor to stop, Frost to Train, then Onaga to stop and his heritage to uncover, but had Smoke never been automated in the old canon he would have eventually grown into his own person and warrior similar to how Ermac had. It happened to all the ninjas: Noob Saibot got a richer back story, Ermac gained moralities and a free will, and Rain became the bastard child of an a Edenian God. His automation was pointless, other than to serve as the backbone for Sub-Zero's story in MK3. It never evolved, never went anywhere, hell the Cyborg form for Smoke only got a decent enough look in when Deception came back out, and then the game after that killed everyone off. There's nothing there to really hold on to. One could say that Khameleon even had a better story than Cyborg Smoke had.

1) The episode depicted his story pretty much exactly the way MK3 described it, though:

Sub-Zero and Smoke are at the Lin Kuei temple (in the game, they had just returned to the temple from Outworld/MK2), and find the Grandmaster signing people up to be Cyborgs, Sektor and Cyrax having already volunteered. Sub and Smoke say no and try to run away, the Grandmaster sends the clan after them. Sub-Zero makes it out but Smoke is captured. Sub-Zero feels survivor's guilt and pain over the loss of his best friend.

Later, Sub has joined forces with Raiden's team to fight off Outworld invasions. Sektor, Cyrax, and Cyber-Smoke show up to attack him. Sub-Zero gets Smoke to break his programming through sheer force of will by appealing to his memories and hidden humanity.

It's the same story. The cartoon is the only time it was actually SHOWN in real-time, though. And despite the shit like geek Nightwolf and the jets and the catchphrases and the other non-canon stuff like the Grandmaster's presence, the army of cyber-henchmen (which MK9 also had, though MK3 never did), and the team not being in the midst of an invasion where the population of the Earth (all non-cyborg Lin Kuei included) has already been killed by Shao Kahn and all that...it was STILL a GOOD story.

And MK9 could've been the second time that story was shown in real-time...only this time, without all the goofy noncanon shit that comes along with Defenders of the Realm like jets and Sonya yelling "It's Kombat time!"...they even could've told it with Sub-Zero and Smoke's roles reversed...and they chose instead to give neither Smoke NOR Cyber-Sub any meaningful interaction or character drama between one another. Which frankly, seems almost incompetent from a writing standpoint. Even if I hadn't seen any cartoons or had any other adaptations to compare it to, I'd be just shocked and confused at the choice to take a situation where a form of mind control has forced someone to be on opposite sides of a conflict from his best friend and not even use it.

2) You keep referring to Cyber-Smoke by what happened to him in Deception. That's irrelevant to a discussion about what should've happened in MK9. MK9 adapted 1 thru 3 and MK3 had a good story for Smoke regardless of what happened to him AFTER MK3. (Much like how MK3 had a good story for Kabal regardless of the fact that Deadly Alliance tried to kill him offscreen and Deception turned him evil...except MK9 actually bothered to try showing Kabal's good story...though I'm personally not a fan of him being a cop or the fact that he died instead of surviving to become a vigilante who hunts down Black Dragons...)

Hm, the way it happened in DofR sounds good, but I can't say it's the same story given everything we know that's happened since MK3. Hardly any depiction of survivor's guilt from Kuai Liang, and Sub-Zero's ending doesn't appear to have happened in any form. I dare say the cartoon's depiction sounds more natural and fitting for how Smoke should've turned out instead of being every bad guy's cyber-bitch.
I definitely agree with you about how they could've played up the Smoke Vs Cyber Sub-Zero story with so many different ways of doing it instead of having CSZ be a "boss" for Kabal of all characters.