You're confusing "did" with "could". Possibility =/= fact. And I think it's cute that people honestly think this level of thought went into a dialogue-less 16-bit platformer.
Again, to see where this "level of thought" could occur, one had to read a number of the different source materials that were available (re: Japanese manuals and etc.). These lil booklets that gave the background storyline DID do more to put some thought into the mythos of Sonic lore, which is why such speculation is allowed to exist.
The Japanese manuals for Sonic 3, for instance, basically foretold about the "Ancient Civilization that built it society around a Stone of Power", that we would actually not see in person until Sonic Adventure. It even foretold how the same society eventually came apart at the seams, once the Elders of the village tried to use the Emeralds for their own desires, and inadvertently unleashed a "force beyond their control". Sonic Adventure didn't invent this plot line, it just expanded on what was already there, since Sonic 3.
If you really want to see this stuff for yourself, go to places like "The Green Hill Zone" or even "Sonic Cult" (if you dare), where translations exist. The source material for these early games IS there, it's just that for the longest, it was only in Japanese, and only in their instruction manuals that Sega put out themselves. But if that doesn't constitute as "canon" for this series, I dunno what does.
You're neglecting a couple of things. One, Sonic just happening to make a return visit for no reason.
Could have been relative to anything relating to either a) gameplay reason or b) an actual legit "storyline" reason.
In the latter case, it was stated in the JP manual for Sonic 3, that Tails had already made a sort of "Emerald Radar" that detected the presence of the Master Emerald. (The giant tsunami that was also reported occurring days before, probably just gave Sonic and Tails even more reason to go out and check it out).
If something up relating to the Emerald was enough to get Sonic out there once, it's likely that something similar was able to do so again. Of course, by that time he arrived, Knux had largely already taken care of things, so he was only able to be there just in time to give Knux a quick lift.
Two, the Flying Battery repeating the exact same flight path.
This one is probably purely a thing relating to gameplay. Again, while the overall storyline did happen, Knux was still limited by the constraints of the game itself. So, for our sake, he had little choice but to go through a number of the same levels that Sonic went through, sometimes in the exact same way.
And three, Eggman does appear in Knuckles's story, in Flying Battery Act 2.
This was DEFINITELY more a thing relating to gameplay, or rather just programmer error, by virtue of the fact that some one probably forgot to sub in (or perhaps, forgot to even make) the "correct" and corresponding sprite to the EggRobot, instead of the unique Eggman sprite.
After all, using the debug mode feature in S3(&K), it's possible to make it so that you can have Sonic meet up with Knux's exclusive EggRobot bosses (and sometimes, vice-versa with Knux). In those cases, Sonic still fights Eggman. With Knux, they obviously didn't think that far ahead, so he fights Eggman regardless.
All that just does more to proof that, even after splitting the game apart, there was still was a lot of details that were "unfinished" about the game. Thankfully, Knux actually meeting up with Eggman for a level (when he shouldn't have) is probably the LEAST of these.
Once again, just because something is possible doesn't mean it's likely. If Knux had the Master Emerald handy, he'd have neutralized the Emeralds as he did in SA2.
You argue that way, but, it's possible that by the time Chaos (who probably knew how to use the Emeralds better than most, probably even better than Knux himself) got what he needed, it was already too late. Thousands of years old God-like being against a 16-year old Echidna. I don't think Knux would have been able to do much with the ME either way.
And to nail the case shut, try looking around when Sonic wakes up. Knuckles is gone, Master Emerald is still there.
Alright, I'll grant you that.
Since you made a lot of redundant writing last time I want to clarify one thing: I am *NOT* by any means whatsoever suggesting that Sega is ready, willing, or intent on bringing such mechanics back. I have no doubt that they are not. But again, that something doesn't return doesn't write out its introduction. The Super Emeralds are not a convenient mechanic to work with, given the special circumstances that they require. Again, it could be likened to seeing Dark Spine Sonic again, what are the odds of running into the World Rings a second time? Not only do the Super Emeralds require all seven Chaos Emeralds with the Master Emerald, but the shrine (new Sonic's not-so-Hidden Palace) is probably a key element as well. The Super Emeralds are immobile, after all, and Sonic notes in SA2 that the shrine's design is likely ideal in harnessing the Emeralds' power. This further reinforces that SA2 is probably the only point where it was even a possibility for them to return, especially when you consider the dilapidated condition of the Angel Island shrine.
The basic thing still is, if they really wanted to bring them back, or possibly even "re-vamp/re-launch" the concept (such that maybe Sonic could possibly obtain Hyper form without the need of "Super Emeralds"), they would have done so by now. As you and I both seem to agree on, they've had a number of opportunities to do as such.
But...they don't. And then the question becomes: it is REALLY a thing that they just can't be bothered to bring 'em back, or was it just a thing that the Supers and etc. never really had that much of a consequence on the overall Sonic mythos, and thus, were basically allowed to be "quietly" retconned/expunged/Superboy-Prime Punch'd out of existence, by the Sonic Adventure re-launch?
As much as they've already down-played the concept of Super Sonic over the last few years, I wouldn't be surprised if the latter was more true than not.
I repeat as a broken record that the existence of Model O holds somewhat more canonical weight than the obtaining of Model OX. There is a difference. Model OX, Model a, and Zero's Ultimate Form (sans Z2) require beating the game to obtain. Model O does not. While its inconvenient location and lack of reference mean Vent/Aile probably didn't go exploring in Area N to nab it, that doesn't mean it's not there. Kinda like how Vent and Aile both exist even though you never see them both in the same storyline (yet). Omega's reappearance is further validated by his presence in ZX's disk database.
While Aile and Vent's co-existence has been proven (thanks to ZXA), Model O is in a different boat, I would believe.
The entire concept surrounding it (and even the ways you could obtain it) was definitely more of a thing of "gameplay bonus" more than anything else. You could have either sought it out, or you could have fought the "Legacy Boss Gauntlet" to get it. Both of which, as of now, have no bearing on what happened canonically in ZX. And I doubt that Inti or the story writer was even thinking along those lines, even though they did give him a little extra "shout-out" by giving him his own Disk (which, for the sake of storyline-wise, could have easily been something relating to the historical figure, rather than anything that occurred in the ZX timeline; after all Omega WAS found in ruins in Zero 3, it didn't say anything about finding him in Area N's ruins specifically...).
But who knows? Maybe Model O does exist. But until we get more in the way of source material to support it, Model O, and anything relating to it/him is probably in the same boat, as the likes of X getting Street Fighter moves in the first two X games. You didn't have to beat the games in order to get those either, but that doesn't necessarily anything more in the way of that they "exist".