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I also kinda look at Hoopa is being something of a genie/jinn kinda Pokémon, but then there's already Jirachi...
There's a lot of differences you could potentially work off of, though. Jirachi appears every thousand years, or appears before a pure hero. Hoopa can appear anytime in any universe/dimension/what have you, and is mischievous - I imagine a granted wish from Hoopa would make you wish you never made a wish at all, or something of the like. I'm sure Hoopa's different forms separate it from Jirachi as well, but I don't know much about the forms.
I agree that GameFreak sucks with legendaries, but it does make things interesting for a fanfic writer.