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I read somewhere that some battling mechanics from the series' first titles Red, Blue and Yellow were still being discovered, with one very meta changing one found just last year. My question is this: what was this mechanic, and what other mechanics were only found after the release of the second generation?

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Please provide a Link and I can expand on my answer that I am about to post.
If anybody wants to expand this out into a full blown answer, go for it. But here are some resources that'll hopefully quench your curiosity. Basically, a Smogon user called Crystal did some research on RBY's mechanics and found information/ bugs with the game that weren't previously known.
a. This post, which announces the mechanic you're probably wondering about. The user found that Pokemon won't be affected by a move's paralysing side-effect if they share the same type as the move in question. The biggest effect this has on the RBY game is that Chansey and Tauros will never be paralysed by Body Slam. http://www.smogon.com/forums/threads/past-gens-research-thread.3506992/#post-5944533
b. This information dump, which contains all the other information the user collected about RBY's mechanics. http://www.smogon.com/forums/threads/past-gens-research-thread.3506992/#post-5878612
I'm unsure if there has been anything else found, but I think that's the bulk of it.
That's enough to answer with, Fizz o3o!
That wasn't a bug or a glitch. It was a gameplay mechanic. I distinctly remember one of the Stadium games talking about same type residual effects in one of those Pokemon class things. This mechanic isn't newly discovered, I mean.
Fresh, I'm not sure that's everything so I felt it was more appropriate to write it as a comment. Glad it's good enough to pass as a full response though! If you want me to write it as an answer I'll do that, though.
And Solember, he asked for gameplay mechanics, so I gave him gameplay mechanics. Neither of us said anything about a bug or glitch. If you're right about this being a known mechanic, I'm confused as to why the entire competitive community treated it like it was brand new and how nobody said, "hey, I've known about this for years." I'm positive that if this mechanic had already been proven to exist, battle sims like PS would've already implemented it. They don't leave out battle mechanics for the hell of it (unless it's formally banned by tier voters) and the community is far too large for knowledge to go unnoticed.
Just another reason not to give credence to the online competitive scene VS real world players, I guess. Everyone knows the mechanic at my RB locals. It is meant to be in the game. Also... you mentioned bugs, specifically.

Seriously... this is the Mandela effect, and nothing more. Play Stadium 2. Or I will find you a screen shot.
http://strategywiki.org/wiki/Pok%C3%A9mon_Stadium_2/Trainer_Class

CTRL+F for the word "residual". I am not sure why people have forgotten this, but it is common knowledge in real battles. Weird how so many people have split so drastically.
Notice "information/ bugs". I only included both to address that fact that it may have been an unintentional addition to the game (no hard evidence directly supports it being intentional nor unintentional). And besides, the Fresh didn't ask for bugs specifically, so I gave him the gameplay mechanics he asked for, regardless of whether or not they are bugs with the game.
I don't really understand why you're using mechanics from Stadium to explain a gameplay mechanic present in RBY. Do they follow the exact same battle mechanics as each other? The article you linked me to only mentions burn, poison and freeze anyway, paralysis isn't mentioned in the table.
I'd still be very surprised if it really took the internet upwards of ten years to catch on to a mechanic that people knew about from the beginning. It's this logic that leads me to believe that Crystal was the founder of this mechanic, or more specifically, the first person to provide hard evidence that it exists. I'm not trying to dismiss the possibility that people knew about it prior to this, I'm only expressing my doubt that things would have happened this way.
That also doesn't make real-life players superior to Smogoners an other online battling sites. There are beginners and masters in each field. Why not give credence to them? Some of them work just as hard if not harder then real-life competitors.
I didn't say superior. I said split And also, the actual screen talks about how things changed in gold and silver and says that moves that have residual effects do not affect Pokemon of the same type.  As for this being hard for you to believe that RBY pros who use cartridges knew about it all along, isn't it harder to believe that a body slam spamming /Chansey, Snorlax, Tauros heavy meta game would take twenty years to realize that not one body slam was paralyzing? Again, this is just a split. I can't imagine this coming up in conversation between the two groups, and from a quick poll of my RBY players, they claim to never use simulators. There is a rift. I'm not arguing. It's clear I'm a different classification of player from the other frequent question answerers. Just because I point out the differences doesn't mean I'm claiming to be better. I just prefer it because it's more challenging and there are prizes and titles to be won, as well as less hacked mon. Some people still have Pokemon in their parties from gen 3.
"Just another reason not to give credence to the online competitive scene VS real world players"

That sure sounds like you're saying real-life competitors are better (or more credible) than simulator competitors. Anyways imma stop this argument because it's gone on long enough.
Just in the gameplay mechanics. Not the participants. But okay.
I also find it difficult that if all these RBY 'pros' knew about the mechanic and not one of them  didn't discuss the mechanic with anyone outside the specific RBY community in any way shape or form, or that not a single person from the specific RBY community is also relevant in any competitive community at all.  I find it hard to believe that the two communities never integrated even once long enough to bring up very meta changing information. My guess is that both parties did know in practice (i.e people have noticed for a long time that pokemon types can't be affected by status of their type) but had no evidence for it, just speculation.
That's possible. Cartridge players use double edge more frequently then online players though, from what I can see compiling data from as far back as 2007, but the move pools became quite similar in 2014. But hey, that's just a theory. A game theory.

The actual answer is that this is a very real example of the Mandela Effect.

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Only a few months ago, Crystal_ made some startling revelations about the mechanics of the first generation. These previously unnoticed mechanics are incredibly significant, changing the way the game has been played since the beginning of competitive Pokémon! This article, written a few months after these initial discoveries, tries to understand how the metagame has changed. The most important mechanical change is that Body Slam cannot paralyze Normal-types. This is part of a general rule that a move's added effect does not affect Pokémon of the same type. For example, Blizzard can't freeze Ice-types. This goes for every status except poison. There are two other slightly less major discoveries; one is too complex for me to explain here, but it's detailed in the link at the bottom** — all you need to know in the context of this article is that it is effectively a buff to Slowbro. The other discovery is that we now fully understand Counter's mechanics. The way it works is that it deals back double the amount of damage currently stored on the damage address, as long as the foe's last move was a Normal- or Fighting-type attack other than Counter. Note that when your foe spends turns asleep, switching, frozen, or fully paralyzed, the damage address does not reset. It will reset successfully when any move that is not a Normal- or Fighting-type attack is used.

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the other discovery, which is kind of complex

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The battling mechanic glitches are there as well. Otherwise, refer to fizz's comment.
I'm not talking about mechanic glitches specifically though. I'm talking about recent battling mechanics
But... there really aren't any recent battle mechanic discoveries. Only recent changes to online RB simulators.
There was the one about Normal-types not being Paralyzed by Body Slam. He means things like that.
That wasn't newly discovered. Just newly implemented. Plenty of gen 1 and gen 2 players knew this. I think it might have been in the prima guides, and when it was taken out for gen 2, the meta changed drastically. It was only recently taken out of some online simulators.