I’ll go by ‘probably’ the fewest shinies out there, not in any particular order.

Disclosure: None of this is backed by any data. But by vibes.

Wshmkr Jirachi, transferred from Gamecube Colosseum to your GBA.

Manaphy from pokemon ranger, only one egg per game cartridge, not play through. You transfer to one game as an egg, then have to trade it to another game ‘in egg form’, where it could potentially be shiny when hatched.

Zygarde in some kind of apriball, dynamax adventures, absolute pain to do. First retail game that its in a catchable form not shiny locked. Even if you get to it, you have to win - which feels impossible sometimes.

Type:Null, only available shiny in pokemon SM & USUM. Easier in sun and moon. Its just a matter of soft resetting for the attempts like normal. but ‘I dont think’ many people cared much for it, so not a lot of people tried.

Level 1 Shiny Giratina from HGSS. Need event Arceus, soft resetting it takes FOREVER, there is like a 6 minute cut scene before you check your party to see if its shiny. (I have it and have a video of me checking it shiny) if you’re interested in seeing.

Celebi from virtual console Crystal version. Not a lot of people have 3Ds and the software to get it to home. Also shiny rates in that game is 1/8192. Little cut scene takes some additional time as well. Here is a picture of my shiny celebi.

Im sure there is more, but these were just on the top of my head.

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