At least 80 Fakemon!
Fully customizable difficulty
Internal Game Randomizers including wild/trainer pokemon, types, moves, abilities, items, evolutions, evolution methods, type advantages, and base stats
Chaos mode where things are randomized on the fly! (Note only works on some randomizers)
In-game nuzlocke with customizable rules/causes
In-game challenge modes. Including a single-type challenge, party size limits, species-name challenge, and evolution limitation challenges!
Battle Factory Mode
Upgraded/Custom Battle Engine - new moves, abilities, effects
Ability Discs - teach Pokemon abilities they would otherwise not learn
New Pokedex with more base stat info, learnsets, ability disc learnsets, and evolutions!
Character customization - 60 outfits with customizable skin tone
No HM moves - field moves are used if any party Pokemon can learn the requisite move
New Casino games! Blackjack and Texas Hold' em
New Casino Prize windows, including customizable Pokemon
Daily Pokemart Specials
City Maps for easy navigation
Journal to track storyline and side quest progress
Custom Poke Ball Types
Achievement system with various categories. Some give game bonuses!
Research unknown species in your Pokedex!