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I think that it's a problem with the arena size that they're willing to give you. This trend started in X and Y and became more apparent in SM due to now having trainers show up in battle. The battles are shown to be close up since you don't have unlimited arena space due to having different routes or fighting in buildings. I never hear anyone mention this, but you have the battle model size for wailord and you have the matine surf size in the same game. They could clearly make wailord a more respectable size, but wailord is just too long vertically for the tiny one on one style fighting stages that they decided ot go with for the game. This isn't just for wailord either. Any pokemon with a long horizontal length was shrunken down. Wishiwashi and most of the large legendaries are other notable examples. Pokemon that were solely vertically tall seemed unaffected like alolan exeggutor and celesteela to a degree.
Now what's the solution for this? Make everything arena sized even if it seems out of place? Limit where you can use large pokemon? Do nothing? With sprites, nobody cared. Games like Battle Revolution didn't have to contend with limitations since everything there is a stadium ground due to the place being a theme park. I'm unsure about Colosseum or XD, so I can't say about that outside of the picture in this thread. Give solutions.