Quoted By:
Regular versions
>XY (Best Pokedex, varied region, new features, fun minigames)
>BW (Best story, nice difficulty, amazing postgame)
>GS (Two regions, aesthetically pleasing)
>RS (Fastest, engaging)
>DP (Slowest, very good region)
>SM (Handholding, lack of features, pandering)
>Colosseum (Kinda slow, different gameplay, Shadow Rush is a pain)
>RB/G (Glitchy, worst graphics and UI, least features)
Third/special versions
>BW2 (Lots of minigames, larger region, nice features, better Pokedex)
>USUM (Lots of features, improved most aspects from SM)
>Platinum (Battle Frontier, improved speed, WiFi Plaza, catch both legendaries)
>Emerald (Battle Frontier, battle animations, catch both legendaries)
>Crystal (Animated sprites, female player, Battle Tower)
>XDGale of Darkness (Vastly improved from Colosseum, more Pokemon availiable, added some extras, Purify Chamber is a godsent, still not as great as a mainline game though)
>Yellow (Literally just Pikachu)
Remakes
>HGSS (Pokemon following you, Platinum features, made Johto enjoyable, rematches, Pokeathlon)
>FRLG (Sevii Islands, made Kanto playable, remixed music is cool, solid games overall)
>ORAS (Delta episode, improved Pokedex, new Mega Evolutions, but the lack of Battle Frontier and other things really made it underwhelming)
Personally, I love 90% of Pokemon games. XY are heavily attacked but they just needed a third version and some more developement. Compared to the other dual games, XY are pretty good, and I always go for special versions and remakes instead (unless I want a 100% Pokedex), except for Hoenn (Emerald and ORAS) and Unova (BW1 and BW2).