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I hate how nearly every gym leader uses a monotype team. If the Trial Captains are just Gym Leaders with a different title then I'll probably drop Sun & Moon.
I like how Pokemon has introduced diversity into their games without making a huge spectacle about it. Gamefreak is super based for this.
Reborn and Rejuvination were great games. The terrain effects made every boss battle memorable and I felt like I was overcoming an actual challenge instead of just steamrolling them with a Pokemon I just caught on the route right next to the city.
Uranium on the other hand was boring and by-the-numbers. Uranium's only memorable quality was the Nuclear type, and only like five Pokemon even had it. I didn't care for a single fakemon in the game, and that's something I can't say about any other game with fakemon in it.
The best fangames are the ones that do their own thing instead of try to make something that could pass off as an official game.