Okay, I think we can all agree this section is a little messy right now...

YES.

Specials should be numbered according to their air date instead of being random

Agreed!

The movies should be taken off the list

If I missed any, please let me know.

The recap episodes that contains scenes from previous episodes should maybe be moved here, which were never aired in the US

The goal is to follow the Japanese airing. So I can't move them without proof that they did not air on TV as part of the regular series.

All the Side Story Episodes (https://bulbapedia.bulbagarden.net/wiki/List_of_side_story_episodes) should be included,

I have to more research and think about it. The fact that many short aired as part of a different shows, both in Japan and in the US, complicate things.

All the Pikachu Shorts listed here (https://bulbapedia.bulbagarden.net/wiki/Pikachu_short)

The ANA flights/Pikachu's Winter Vacation shorts are fine, but the theatrical shorts shouldn't be in the specials.

-Hoopa's Surprise Ring Adventures should be included (https://bulbapedia.bulbagarden.net/wiki/Hoopa%27s_Surprise_Ring_Adventures)

Road to Kalos, a special recapping a lot of things before the first episode of Pokémon XY aired

Anime-styled shorts and trailers to promote the game could also be included

Probably not. Feel free to provide links and/or plead your case though.

I'm not so sure about these ones, but maybe Pokémon Origins (https://bulbapedia.bulbagarden.net/wiki/Pok%C3%A9mon_Origins) and Pokémon Generations (https://bulbapedia.bulbagarden.net/wiki/Pok%C3%A9mon_Generations) could also be added even though they are already listed as their own separate series on TMDB

I'm fine with keeping them as individual series.

If I missed any, please let me know.

Think you got all of em! =)

The goal is to follow the Japanese airing. So I can't move them without proof that they did not air on TV as part of the regular series.

Cool! I just thought that it made sense to put them under specials because of how the Pokémon episodes are divided here on TMDB, following the American season models instead of the Japanese division that's pretty different (the equivalence and differences can be compared here). These recap episodes are not officially included on these American seasons division model since they were never aired on the US. For instance, if you check the Season 8 episode list you can see that AG120 (currently S08E28 here) is skipped, and the season ends up with 53 episodes here instead of 52 as in the official division. Same happens with end-of-saga special episodes, for instance. Season XYZ has "The Ultimate Duo! Citron and Dent!!" included in it even though it never aired in the US, which means it's not on the official season episode list.

The fact that many short aired as part of a different shows, both in Japan and in the US, complicate things.

I mean, technically they all aired as "Side Story Specials" in Japan... if the goal is to follow the Japanese airing, wouldn't it be okay to just use the Japanese model?

the theatrical shorts shouldn't be in the specials.

Really? That's unfortunate... is it because they were aired with the movies? Do they have to be considered

Probably not. Feel free to provide links and/or please your case though.

I think it would be fine to leave them out, I just don't know where these short specials could be put though. Just added as standalone episodes, without a series? Some of them are already on the specials section at the moment, like the Mystery Dungeon ones and Pokémon Ranger: Guardian Signs, so I thought that if some of these specials promoting the games were already there we might as well include all of them.

I'm fine with keeping them as individual series.

Oh, totally! I don't even know why I suggested this one back then, keeping them separate is much better.

Anyway, here's a list I made sometime ago when I was organizing my files of all the things I suggested on my original post (except Origins and Generations, I left them out) in their respective original airdates, so the final list probably could look like something like this I guess. However, the things you mentioned should be debated whether or not to put in the list, such as the theatrical shorts, recap episodes only aired in Japan, and specials to promote the games are in the mix, so of course some of the items in the list maybe are not going to be in the final cut. https://docs.google.com/document/d/1s_qu4iQG4F1CM04UNgCsoBzFhGfsuxn3UCujaLftRtQ/edit

Oh, and just one last thing I noticed: "The Birth of Mewtwo," which is showing up as the first episode of the list, should actually be "The Uncut Story of Mewtwo's Origin," which aired in July 8, 1999, which was an ADAPTATION of the radio drama "The Birth of Mewtwo." The title and air date it currently has refer to the radio drama rather than the short.