Bulbagarden Forums gives us a rundown of actual gameplay changes to Pokemon X and Y. Never mind what parts of the game are 3D or not, this is the part of Pokemon that will actually affect your experience whatever your preference.
First things first, capturing wild Pokemon will now net your Pokemon experience, the same number points as you would get in a normal battle. Experience in Pokebattles has been reverted back to Generation 1, meaning all Pokemon get the same level of experience after one Pokemon in their team wins a Pokebattle.
Sky Battles are very restrained. First off, only who can Levitate or are Flying Type can enter Sky Battles, and some moves are unavailable.
The Breeding system, particularly how traits are inherited, has been adjusted.
Ghost Type Pokemon can run away from battles, even if the opposing side uses Shadow Tag, an ability that restrains Pokemon from escaping.
New Pokemon were put on priority in terms of getting new moves and abilities, but they did look at everyone when revamping the power and accuracy of some moves, particularly the specials.
They also shared more details regarding Mega Evolutions. Apparently, not all Pokemon have Mega Evolutions, with priority places on those who have a suitable look, are popular and can help balance out the game.
When Pokemon are powered up to Mega Evolution level, they get powerful enough to match legendary Pokemon. For this reason, Mega Evolution has been restrained, with only one Pokemon able to hold a Mega Stone in a battle, and the timing for Mega Evolutions not available at all times, although it is selectable.
Finally, Game Freak explained they reverted back to a cuter style for Pokemon X and Y, compared to the more realistic look of Pokemon Stadium and Pokemon Battle Revolution, as was befitting a handheld version of the game, which is meant to be played by everyone.
Source: Bulbagarden Forums
