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 Cinnibar Island. Mewtwo is still in Ceurlean Cave. You can now catch Entei, Raikou, and Suicune after deafeating the Elite Four, roaming around the region. You can catch Entei if your starter pokemon was Bulbasaur, Raikou if your starter was Squirtle, and Suicune if your starter was Charmander. Lugia and Ho-Oh can be caught with the event item the MysticTicket, which, after the Elite Four can be accessed by going to the harbor with the ticket. You can catch Deoxys with the event item the Aurora Ticket, which will bring you to Navel Rock from the harbor. You will catch it in Attack Form in Firered and Defense Form in Leafgreen.
Move Changes
Movelists are updated and include the moves added in generations 2 and 3.
The TM list is the generation 3 list, not the generation 1 list.
Move tutors are now available and can teach pokemon generation 1 TMs. Three new move tutor moves have been added. Blast Burn, Frenzy Plant, and Hydro Cannon can be taught to the fully evolved Kanto starter pokemon's final forms from the move tutor on Sevvi Island 2.
New Devices
Trainers that are outside now can be rebattled due to the Vs Seeker.
Information on major characters such as gym leaders are stored in the Fame Checker.
A Help feature has been added. It can be accessed by pressing the L or R buttons.
Other Changes
The Elite Four can now be rebattled. After completing the Sevvi Islands Quest, they will have generation 2 pokemon as well as generation 1 pokemon.
Team Rocket has a new base on Sevvi Island 5, making them the only villanous team that does anything after the Elite Four.