PokéBase - Pokémon Q&A
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I have recently been playing my copy of Crystal and have been wondering about the differences in battling , EVs, if moves do the opposite of what they are supposed to do (Focus Energy back in gen 1) or are broken (like Wrap), etc. compared to Gen 6 and its style of battling.

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mega evolution and fairy type immediately come to mind. As well as ghost and dark not being very effective against steel in gen 2
Physical/Special split as well. Critical hits are no longer based on Speed.
Crits were only based on speed in Gen 1.
The list would be impossibly long.

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Best answer
  • Mega Evolution and Primal Reversion
  • Fairy type
  • Physical-Special type shift
  • Dark and Ghost type do normal damage to Steel types,
  • A new system for EVs gained was introduced
  • Abilities
  • Natures and characteristics
  • Greater variance in IVs (0-31 rather than 0-15 as it was before)
  • Personality Values
  • Shininess no longer depends on IVs
  • Poison status doesn't hurt while you walk
  • Sleep lasts less turns
  • Electric types cannot be paralyzed
  • Ghost types cannot be trapped
  • Grass types are immune to powder moves
  • TMs are inexhaustible now
  • Move Reminder
  • Number of items the bag can hold was upped to infinity
  • Double, Triple, Rotation, Sky and Inverse Battles
  • Horde Battles
  • The number of boxes available was increased
  • Ability to move multiple Pokemon in boxes
  • Experience on catching Pokemon
  • The ability to actually plant berries now
  • The ability to run (Technically because of running shoes but that's a huge improvement!)
  • The ability for the player to walk in an 8 directional grid as opposed to the 4 directional grid
  • Pokemon Amie and Super Training
  • All Pokemon got a custom screen sprite
  • The Apricorn system was abandoned
  • You can actually see some stuff without Flash, earlier it was just black
  • Moves that require you to charge after use (eg.- Hyper Beam) no longer allow you to switch if you faint a Pokemon
  • Weather can now start without a Pokemon responsible (sandstorm in desert, hail in snowy place, etc.)
  • Less capitalized stuff (Pokemon instead of POKéMON, Solar Beam instead of SOLARBEAM)
  • Pokedex was upgraded in many levels
  • Ribbons
  • Different sprites for gender-differentiated Pokemon
  • Eggs hatch at Level 1 instead of 5
  • Animated sprites
  • ???-type doesn't exist (Curse, originally a ??? type was changed to Ghost)
  • Pokemon can evolve even if the Pokemon/player was knocked out/whitewashed
  • The Experience Underflow Glitch is fixed
  • The use of internet to improve battling and trading (Battle Spot, GTS, Wonder Trade)(Credits to Astro)
  • No more of Whitney's Miltanks <3

That's as much as I know, let me know if I missed something :P

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Battle Spot, GTS, Wonder Trade. Basically improved trading.
I dunno if I should include that because it's not really an in-game mechanic...
Screw it, thanks :3
Ehhh, no problem buddy ;D
Thanks, nice list
Added a bit more that I remembered while I was asleep :P
And no problem!
You forgot natures and characteristics ;o
I accidentally cut that out in editing xP