I found a link to that thread on the Bulbapedia page of Generation I index numbers.
I agree with you that they should have found a way to incorporate the unused elements by now, but as I see it, they got sidetracked with remakes in the previous two generations. The first thing I'd like them to do now is to release a Unova sequel in this generation; I don't expect to see any unused concepts there (except for that Mewtwo event) due to the nature of this generation, but if they made a point of addressing all of Unova's mysteries as I believe they were going to do for Johto, it would be a positive sign about the future and possibly the past.
I don't think that Pokémon X was in development along with Ruby and Sapphire. While the title may have been tentative, the game was supposed to be released in April 2000 and then pushed to late 2000 or early 2001 (it turned out to be the former). Did Game Freak consider using the unused elements in Ruby and Sapphire? In early 2001 they certainly might have, but I think that by the time the Mobile Adapter did not turn out to be successful (say in the middle of 2001), they decided to change many things, if not everything. If I'm right about the 25 Pokémon, Game Freak may have decided to scrap them because their events couldn't be done without the Mobile Adapter, at least not in the way Game Freak wanted.
You could argue that the e-Reader was an alternative to the Mobile Adapter, and indeed, at least Latias and Latios (whose prototype might have been designed for Pokémon X) received an event that way. But Game Freak didn't even use the e-Reader to make the missing old Pokémon available, and after Ruby and Sapphire the concern was making those Pokémon obtainable again, rather than dealing with any additional Pokémon.
Come to think of it, maybe they considered releasing a game in the vein of Pokémon X after Ruby and Sapphire, but the decision to remove backwards compatibility made them opt to remake Red and Green instead. Again, something like that would most likely have been decided in 2001.
This isn't directly relevant, but there is something in Generation I that I've only just found out: There are only 39 Missingno., with the other 66 index numbers being garbage data. Why is that important? Because Shigeki Morimoto confirmed that there were, in fact, going to be 190 Pokémon in Generation I.
If you read that entire thread, you'll see that the person who made this discovery was most likely wrong about the original Pokémon being the Generation II Pokémon that correspond to the Missingno.'s index numbers (in particular Ho-Oh, which Morimoto said was not going to be included in Red and Green). But Morimoto did say that the designs had been scrapped to be used later.
Morimoto is the one that should be on Twitter. Then again, in the HGSS interviews he was more talkative about the first generation than the second one...
There may be leftovers from Pokémon X in Generation III. There are 25 missing index numbers in the GBA games - the ones between Celebi and Treecko. If you read the discussion here, someone theorized that the additional 25 Unown letters were originally independent from Unown A, only to be erased when Game Freak decided to use the personality value to determine Unown's shape. What that person failed to take into account is that (unlike the Deoxys Formes) the 28 Unown shapes do have separate index numbers, with the last 27 being located at the end of the list (although the only data associated with those numbers is the sprites). It is unlikely that Game Freak just moved the 25 Unown letters for basically no reason at all.
I think it is completely feasible that Game Freak imported some of the old data from the GBA version of Pokémon X they had partially developed, meaning that those 25 slots represent unused Pokémon. 25 is not a bad number, although I could have done with more.
I was mostly referring to the third and fifth questions. Game Freak have never really shown us that there is an alternative goal to being a trainer; certainly being a researcher would count as a goal, but unfortunately, the only prominent researchers in the games are the professors that rely on trainers to complete the Pokédex, which is an optional objective that has almost no effect on anything. Because of this, the idea that Chieko wanted the player to expand their horizons is surprising in my eyes. It's as if she said that even an exceptional trainer did not deserve to hold the GS Ball unless they had an additional goal. It could also be argued that she was suggesting that protecting and rescuing Pokémon was one such goal. Granted, that is usually the case in the games when the player fights the villain, but it has never been described as a goal (arguably except for Black and White) and seems like a hazard the player is forced to deal with.
Then there is the fifth question. It was probably in reference to the Brass Tower legend, as well as the Ruins of Alph's history as a place where the Unown shared their insight with people. These are things that were told about in Crystal, but not shown. So players would have been rational in thinking that the stories may have been embellished, but had they believed that, they wouldn't have been eligible to receive the GS Ball. In contrast, Cynthia did see Dialga, Palkia and Giratina before her very eyes, but she still doubted that their myths about their powers were a realistic description.
A long time ago, I wonder what sort of person painted this? Dialga's Roar of Time... Palkia's Spacial Rend... To the people back then, those Pokémon really must have appeared to rule over time and space. Seeing them must have shaken the people to their very core. This painting represents those feelings of awe, wonder, and everything else. It passed that memory to countless people, eventually becoming a myth...
It's hard to tell which Generation III might have been designed for for Pokémon X. There was a two-year gap between Crystal and Ruby and Sapphire, which would have been enough time for Game Freak to work on the latter games completely from scratch. The Mobile Adapter was sadly not a success, so in a way Game Freak abandoning their unfinished project was excusable. Overall, I'm inclined to think that most of the Pokémon X critters would have been those that had been scrapped from Gold and Silver, which would explain why Pokémon X was originally scheduled for a very early release. I obviously don't know how many new Pokémon would have been involved, but the Gold and Silver information from Spaceworld 1997 suggests that over a dozen Pokémon were left out of the final games, and the real number could be easily close to 50.
There is one thing in the beta Ruby and Sapphire information that suggests a link to Pokémon X. While the creature in this artwork is an obvious prototype of Blaziken and Latias, the girl resembles Kris. It is possible that the design actually pertains to Pokémon X, and the connection to Ruby and Sapphire is limited to the fact that the design inspired Blaziken and Latias.
Here are the questions Chieko asked in one of the months she was in the news:
1) Should Pokémon be protected and rescued by people other than their owners? [Yes]
2) If a Pokémon is afraid of a person, is it the person's fault? [Yes]
3) Is there a goal for a person who likes Pokémon beside being a trainer? [Yes]
4) Is a child a weaker trainer than an adult is? [No]
5) Do you think that the legends from the days of old are all a lie? [No]
You probably agree that this hints at a deeper story. These questions are quite unlike anything else in the games.
I'm primarily interested in what could have been. I'm not going to abandon this research just because it seems unlikely that Game Freak will incorporate the scrapped elements into future games; we don't know what Game Freak have in mind for the next generation, let alone the next 15 years.
I will say this: HGSS are remakes, and therein lies the problem. In a way, the remakes stayed true to Gold and Silver's story even more than Crystal did, for the sake of nostalgia. Does this mean that Game Freak have no interest in expanding the Johto story? I don't think so. The two HGSS movie events (the Sinjoh Ruins and Giovanni events) established two important things that were vague in Crystal: 1) The Unown have an important but unknown role in the Pokémon universe; 2) Celebi uses time travel to prevent terrible events.
Will Game Freak leave it at that? I don't see why they should when these concepts could easily fuel a brand new game with very unique elements; Johto wouldn't have to be the setting because the legends of that region are universal. I know that you don't subscribe to the theory that Game Freak will never stop remaking old games, so what do you think they may do instead to keep the past relevant?
What I've recently discovered is that there is more to the GS Ball event than what we western players could have imagined. Every month throughout the Mobile System's activity, Crystal's News Machine was updated with a news feed that included a mini-game and/or quiz. In the months when the GS Ball was distributed, the text-based mini-game and quiz were assigned to a character by the name of Chieko, who described herself as a ball expert from Azalea Town. Since Kurt's grandaughter (Maisy) is called Chie in Japanese, it is obvious to me that Chieko is an adult Chie from the future. What I now want to find out is what exactly Chieko said about the GS Ball, and whether or not there were other mysteries hinted at by the News Machine. For that I need a Japanese game that not only received the News Machine updates, but also has a working save file.
My theory is that time travel was supposed to be the main theme of Pokémon X, but since Crystal was a reduced version of the initial concept, Game Freak settled for hinting at a time travel story.
I don't mind stalking; if I did, the messages would be private. The only problem is that I don't know how much you've read.
In a nutshell, a GBC game called Pokémon X was announced by Nintendo in December 1999. The game was scheduled for an April 2000 release, but was said to have added features unlocked by the GBA (which was then going to be released in August). More importantly, Nintendo did not just say that the Mobile Adapter would be used for online battling and trading, but also for downloading new Pokémon. In March, Nintendo reported that both Pokémon X and the GBA had been pushed back to late 2000 or early 2001, and that the game was now a GBA title. By June, Nintendo's president stated in an interview that Pokémon X would be released for the GBC after all; while he noted similarities to Gold and Silver, he still mentioned the new downloadable Pokémon (he also separately discussed the Celebi download for Gold and Silver, so Celebi was not new by that time). The rest is, as we say, history. It has never been revealed why Crystal didn't feature new Pokémon, but at least Yamauchi clarified in early 2001 that Game Freak had unsuccessfully tried to develop a GBA launch title, so their GBA efforts shifted to a brand new generation.
What it is I want to know is how exactly Pokémon X was different from Crystal. What would the new Pokémon and GBA features have changed? I find it hard to believe that the story would have been identical.