Magnus owned Bahamut pokemon, but that was given to the E4 to use
There was going to be a trio legendary that roamed, they would be rock looking Pokemon that floated.
Many legendaries were going to appear but many were cut, some are still appearing.
There was going to be an ogre and troll Pokemon
A floating barbed bomb like Pokemon called "Smeltox" would have appeared, it would be Poison/Steel.
The third mythical was originally going to be a manifestation of acid/poison that looked like Chaos from Sonic but it was replaced with the Hydra
There was going to be a water salamander pokemon (Torrander/Atlandas) that would have been version exclusives with the Swordfish Pokemon
The third mascot was going to be called Byagroth, it would have been Dragon/Steel
Many evolutions of existing pokemon were planned, notably Sableye, Sandslash, and Dugtrio until they got Mega Evolutions and Alolan Forms. So they never happened.
There was going to be a fire bull Pokemon, was scrapped. Eventually the idea became the Fire Starter.
The fire starter was going to be the horse instead (it would have been Fire/Steel), but the typing was changed to grass.
The fire starter was originally a fire type koala until Komala was announced.
Qwilfish was going to evolve (although that may still happen!)
The gym leaders were going to be Flying/Electric/Bug/Water/Poison/Steel/Dark. Only the Dark and Steel still exist, the Dark Type guy is an E4 and the Steel type is the last "trial captain"
Weezing would have evolved (although that may still happen!)
The mascot duo was Agielem and Zegrygale, under different names.
The region was going to be called Aona
The Magnus and Apollo were the first characters that I came up with, they always were brothers from the beginning. There was going to be a flashback about how Apollo was going to be the king and not Magnus and that is why he chose to be evil, this was scrapped and replaced with Typhon corrupting Magnus. The king would be someone else but he will not appear at all, but you can still visit the castle.
There was going to be the "100 in all stats/mew" pokemon that was some sort of Psychic/Dark dog.
The E4 was going to be Ice/Fairy/Fighting/Ghost. Only the Fighting and Ghost specialists still exist and have a role.
Some locations were removed
Some Megas never existed too, Z-Moves were never planned
Doge would have been a pokemon.
The Macaw Pokemon was removed recently
A multiple form human pokemon was added late in the production, they are humans manifested by crystals so they are mindless crystal creatures now considered pokemon.
Shuckle would have gotten an evolution but was removed because Eviolite existed
When revising the game the legendaries were supposed to be called "Ancient Beasts" but it was removed because it was unnecessary.
Later in production the regional bird was gonna be Flying/Ground but now it is Flying/Steel
Some other scrapped pokemon were a garden mole, platypus (specific types depending on gender), centipede, a dead human ghost, lapras pre-evo, Vermilion Bird (which could still be in the game but maybe not), and the legendary trio would have been minotaurs specializing with the ground type.