Features
A dex full of fusions, 376 to be more precise, all of them obtainable.
Mega evolution added (yes, some of the fusions have megas).
Custom Dex entries for every fusion, as well as the base stats on it.
Some of the HMs have a different typing and effect (like Flash 60 power and electric type).
Forgettable HMs.
Infinite TMs.
Physical and Special Split.
Fairy Type, and Fairy Type moves added.
The last Gym leaders as well as the Elite Four and Champion have Megas.
Increased Shiny odds (1/257).
Added the item Link Cable to evolve Trade pokémon.
All the wild pokémon changed due to their design or lore.
Your pokémon won't die to poison outside of battle
Gen 5 Repel
Added difficulty
Move relearner in every Pokemon Center