Holy crap, there's a lot of stuff here. Firstly, I revised Glitch-type. It is weak to Psychic, Fairy, itself, Celestial, and Water (first two because order, itself because well, duh, and Water because what happens to electronics when you expose them to water?) though you can ignore Steel.. It is resistant to Electric, Dragon, Flying, Poison, and Steel (Electric+Steel because machines, Dragon and Flying because it's kinda like Electric and Dragon's like Flying, and Poison because it's a glitch, how would you poison it). It should be immune to Steel, but Celestial is immune to Steel in my game, so I didn't want to debuff it that much. It is super effective on Electric, Steel, Dragon (aura-type to some extent) and itself (duh), while not very effective on Psychic, Fairy, Dark, Water, and Celestial, and again, you can ignore Celestial.
Second, 20 gyms and 20 HMs? Are you my friend Alex? Just kidding, but honestly, I think that your game will take a LOT of work. Did you misspell Johto or Kanto the first time or is Kohto a region in the game? And I think that anime obsession's a bit weird but I don't really care. Just don't make Iris an annoying weirdo like in the BW anime and I'd be fine.
Third, yes, Gyms can exist without HMs.
Fourth, I think an Eeveelution for every type is a bit ridiculous (look who's talking, creator of Veneon, Spectreon, Brawleon, Litheon, Wyvreon, Ferreon, Cloudeon, Quakeon, Lucideon, Mega Lucideon, and Astreon?) but go right ahead. Might I suggest having each gym use an Eeveeution then? Like, as the first Pokémon of the leader's team.
Fifth, Trials with HMs is that the little NLT amulet gets a mark for each trial, which means somehow that you can use HMs outside of battle (or maybe I'll just make the HMs inaccessible until you get that mark and the mark proves your strength, thereby accomplishing the same thing in a way that makes more sense and I can simply say you can use HM moves regardless of number of badges in the code). Except in the case of Cut, which is given to you for use in the Grass-type Trial. And I also will try to make two more HMs because NINE trials, but currently SEVEN HMs.