Oh boy, the little things made this game.
Search function in the boxes - life saver
Dragging multiple pokes in boxes - read above
repel chaining - yes sir
medals - a step towards modern gaming
free space - better customizable organization
join avenue - what's more fun than leveling up your pokes? Leveling up your shops!
key system - difficulty and trading cities was very cool and a step up
Unova Challenge - A rogue like (kinda) feel tower exploration game that was actually challenging and engaging post game, really enjoyed it.
New breeding mechanics - makes us breeders have less headaches
Real rewards - charms, shinies, a lot of cool stuff.
its the small things - again, so I can't really think of all of them now, though I assure you it is more than what was said above.
Stuff that was new but were underwhelming -
Pokestar Studio - meh
I guess that's it. Though GF did streamline a lot of the game mechanics, trading pokemon and items is still a chore, GTS is useless, random matchup is a nightmare, anything that has to do with player interaction (what this game was built upon since Red and Blue) is soo tedious, and nothing was changed on a large scale. Hopefully Gen 6 will fix up this series to be on par with its contemporaries, GF is lucky that this is pokemon, and they can get away with a lot of their annoyances, i.e. pokemon is so awesome, most of these faults can be overlooked, but not for long.