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Mom & Dad, just Dad, or neither
Two professors (one for each version, two in third)
Female Antagonist group leader
Two Champions (depending on gender)
Completely different story line per version
The ability to be challenged as champion
SEARCH IN PC!!!!!
Pokemon follow you but it doesn't have to be the first one in party
More season/weather variations
Auto-run like HGSS
More touchscreen actions like HGSS
Jump two years into the future after completing the game
Choice of ending (defeat evil Team/Champion)