Just taking a look at the Pokémon go set and seeing that mewtwo cards account for almost 6% of the entire set. I love mewtwo because of the first movie, so I’m not complaining.
It does have me wondering what is the highest occurrence of a Pokémon in a set? Pikachu in Celebrations is obviously massive, but it was the anniversary and pikachu is the face of the franchise.
Outside of that does anybody know?
Deoxys has 6 different cards in EX Deoxys. If that’s not the highest, it’s gotta be up there.
7 different Charizard’s in Flashfire
Platinum Arceus has 12 Arceus cards
Actually, Platinum Arceus has 12 different Arceus cards, making up roughly 10.7% of the total set.
I believe second place goes to XY BreakThrough which has 10 different Mewtwo cards, which is also roughly 6.06% of the total set.
@alecpokemon mentioned Flashfire having 7 different Charizards, which is roughly 6.4% of the total set.
Off the top of my head, a few sets give 6 cards to one Pokemon - @zorloth mentioned ex Deoxys, but there’s also XY Roaring Skies (with 6 Rayquaza), BW Boundaries Crossed with 6 Kyurem, SM Ultra Prism with 6 Necrozma, SwSh Fusion Strike has 6 Mew, SwSh Brilliant Stars has 6 Arceus, and technically BW Noble Victories has 6 Victini if you count the prerelease and staff variants. I might’ve missed a set or two, those are just the ones I can remember off the top of my head.
Once you get to 5 cards of one Pokemon per set, you start moving into modern alt-art territory. Many Pokemon have 5 if they get a V, VMAX/VSTAR, FA, Rainbow and alt/secret prints. It’s fairly common from XY-onwards for some Pokemon to have 4 or 5 cards in a set.
Oh of course, can’t believe I missed the Lv. X’s 
EX Unseen Forces/Golden Sky, Silvery Ocean with 30 Unown wins for sure.
The 12 Arceus from the Arceus set are probably second.
And I forgot about the 10 Mewtwo from BREAKthrough, which is probably third!
As for EX Deoxys, I’d argue there are 9 Deoxys cards in the set instead of 6, since three of them have Reverse Holofoil variants. And I personally wouldn’t count prerelease or STAFF cards, since those were not actually part of the set itself and simply a variant. Otherwise Shining Legends contained 7 Pikachu, even though only two came from the set itself (non-Holo and RH), and the Base Set Pikachu might give the EX Unseen Forces Unown a run for their money. 
As for some other sets with six of the same Pokémon I could think of:
Greetz,
Quuador
Haha now this is gonna be controversial
Where do people generally lie with this interpretation. Wouldn’t mind seeing a poll if someone creates. Technically the same Pokémon, but how do we feel about the different variants.
Are they variants like we see with aloan/galarian/mega etc.?
or
Is each one a unique pokemon?
Is the lore clear on this haha?
Yeah, I kinda see the different forms as different Pokémon as well in most cases. But tbf, that disqualifies almost all the other examples named thus far as well: Arceus had different Plates in the Arceus set; Mewtwo has two different Mega Evolution forms in BREAKthrough; Deoxys has different forms in EX Deoxys; etc.
As for one more example, since I see you’ve mentioned the 6 Pikachu from the Celebrations set: the Japanese/Thai/Indonesian 25th Anniversary Collection set has 10 + 1 RH Pikachu cards.
Greetz,
Quuador
Unowns probably win
I hear some special sets of 1st edition base can have up to 396 Gijoemon, so I’m guessing that maybe?
not highest, but most recently pogo has 4 dragonites.
Some honourable mentions regarding promo sets
2009 Card Design Contest
Arceus x7 / 13 = 53.8%
Pichu x6 / 13 = 46.2%
2010 Card Design Contest
Zorua x6 / 10 = 60%
Zoroark x4 / 10 = 40%
Art Academy Competition
Pikachu x12 / 22 = 54.5%
2010 Pikachu World Collection
Pikachu x9 / 9 = 100%