Game Freak/Nintendo has gone out of its way to say no evil Pokémon exist, they're bad only because they have bad trainers, but there's
wild Malamar shown in the anime to have actual evil intentions. So which is it, Nintendo?
How did it take so long for fairy types to be discovered when there was a fairy type 1000 years ago in kalos?
It's possible the Fairy-typing was always a thing (such as with Clefairy), but researchers needed more proof to confirm it to then announce it to the scientific community.
Valerie, Kalos' Fairy-type gym leader, originates from Johto, so she may have decided to be the "special snowflake" (she honestly looks like someone who'd think that way) and take up residence in Kalos as such. Laverre City may-or-may-not have had a gym before her; if they did, she may have challenged them similar to how Sabrina challenged the Fighting Dojo to take over as Saffron City gym leader.
Are there multiple regi pokemon? They're golems so they could be artificially created.

And they were locked away by the ancient people because they feared them... Would these be the same ancient people who created the Ruins of Alph? We have the Sinjoh Ruins, after all, which connects Johto and Sinnoh, and Regigigas hails from Sinnoh...
How are hamburgers a thing? Unless there is an actual hamburg and it isn't change crumbella town or something.
Think it's actually confirmed humans
do eat Pokémon, and any time they do eat meat, they eat everything out of respect for the slain Pokémon. Wouldn't be out of place for beef patties to be made from Tauros.
What is the percentage of people who live with pokemon or are pokemon trainers? there seems to be a lot but how does the society sustain itself?
There's still an economy with the currency used (which appears to be a unified currency), and Ryme City in
Detective Pikachu is explicitly stated to be unique in that it's a place where humans and Pokémon co-exist, although Fortree City is supposed to be that way as well. There's police departments, and the Pokémon Centers may actually be sustained by charity, and in the anime there's some mention of politicians, so there has to be a working government. Normal jobs exist in the Pokémon world, and I don't think all of them have Pokémon helpers. People who keep Pokémon as pets don't battle with them, but not everyone has a pet.
And not everyone can become a Pokémon trainer, it's apparently one of the most grueling, albeit rewarding (?), career paths out there, and there's rankings for trainers, it seems. Although in Takeshi Shudo's novelization of the anime, gym leaders can be kicked by the organizers of the Pokémon League if they lose too many times.
If shinies are recessive genes how come there are no other recessive genes like blindness, dwarfism or exceptionalism?
Mini-Dit in the anime is shown to have problems with Transform in that it cannot replicate the actual size of Pokémon bigger than it, suggesting a recessive trait (not necessarily dwarfism).
In
Let's Go, Pikachu/Eevee, Pokémon of any species can be tiny or large, so there's a wide range of sizes Pokémon can be like real animals. So it wouldn't be too out-of-place for there to be Pokémon with birth defects or other recessive traits, but they might not survive out in the wild (obviously).
If every Yamask has their original deathmask attached to themselves, does that mean all yamask were significant people in ancient Unova or was at just common for them to do that?
I have a theory that all living Yamask may be descendants from a Cofagrigus who was partnered with a beloved king/leader who passed away and became "one" with his Pokémon. Its children were then born with death masks meant to represent that human, and although they never knew the leader personally, genetically they're still linked to "recognize" the death mask. Think of how crows recognize people's faces, and even their descendants are taught to recognize the same face--though I don't know if it's because they tell them in great detail, or it only "works" because that person stays in the same area the whole time and crows, holding grudges, gossip about it even to their children.
Are the fossil pokemon accurate reconstructions of their prehistoric selves or is it possible that none of them are originally rock type and its fossilization that caused that change?
It's all but officially confirmed ever since Genesect was created that the dual-typing may be the result of the resurrection process (although let's face it, they're actually clones). Genesect was modified with a cyborg body to have the Drive on its back during the cloning process, giving it the Steel-typing. Whether Genesect can actually breed like the other resurrected prehistoric Pokémon, though, that's up to the fans to decide.
How come some pokemon aren't elevated in higher parts of society than humans? Alakazam seems like they should control the world because they're all so smart.
Sinnoh myth suggests Pokémon are to be at the ready to help humans, hence why wild Pokémon pop out of the tall grass, but humans may still be considered the dominant species. World leaders may have Pokémon of their own that do their bidding for all we know.
How come the police all use growlithes? Wouldn't fire pokemon be more dangerous to the job?
Probably for canine patrol, though
Generations showed they can and do use other Pokémon for various situations.