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I'm not sure what you mean: are you talking about websites that host Pokémon games, or other tools used to make Pokémon games? (I'm not sure what you mean with "websites that are used to make Pokémon games")
There are lots of other sites that host fan-made Pokémon games. I don't know them all, of course, but Relic Castle seems to be the second most famous after PokéCommunity, and both of them not only host fangames, but they have a developper community to help other devs.
As for the tools, basically there are three engines for making Pokémon games: RPG Maker, decompilers, and ROM hacks. Some people talk about Unity but it doesn't exist yet.
As far as I know about it (which isn't alot), the only thing I've seen Unity used for is modding BDSP on the Switch. I haven't seen any drastic mods to say that they are creating romhacks or fan games though. But I guess the possibility is there.