>>25336156New engine/mechanics as well as the graphics. Also trading/battling.
Gen 2 is obviously separate from gen 1 because it has a different stat and 2 new types. Also IIRC you can't battle gen 2-gen 1, only limited trading
Gen 3 is separate engine from gen 2 because entire data structure is different and abilities/natures got introduced.
Gen 4 is separate because physical/special split. And again, you can't directly trade/battle with gen 3.
Gen 5 can't directly trade/battle with gen 4, exp scale got changed, ??? type got deleted
etc etc
The theory gen 6.5 supporters are using is that with Sun/Moon, even if it introduces new Pokemon and takes place in say, Southern Kalos, you'll still be able to directly trade/battle with other gen 6 games as long as you're using compatible Pokemon the same way ORAS-XY only worked with compatible megas/abilities/moves. Also the graphics will be the same.