Pokemon have natures, abilities, genders, and can hold items.
The Pokemon have their generation 2 and 3 evolutions, but cannot evolve into them without first obtaining the National Pokedex. An example would be Golbat evolving into Crobat.
Magnemite now are Electric/Steel type.
Pokemon can now breed in the daycare on Four Island, and still can go to the daycare on Route 5.
Version Exclusive Pokemon and wild pokemon have now been changed because of new evolutions from generations 2 and 3.
Legendary Pokemon have also changed. Articuno and Zapdos are still found in the Seafoam Islands and Power plant. The location of Moltres has been changed from Victory Road to Mt. Ember, which is on Sevvi Island 1, which can be accesed after deafeating the 7th Gym on