Gen3 is the black sheep of the series, having been made at a time where water games were in (Wind Waker, Sunshine... ect). I love them though. 2nd fave gen by far, with GSC being THIRD (IT'S OVERRATED PEOPLE! Time is not THAT GOOD of a function!), and DPPt being first. (The new pokemon either look cool, or at least are creative, unlike the Gen1 stuff)
The reason it isn't liked is the nonsence plot (In a pokemon game... yeah. And GSC's was far worse), and the sheer ammount of water (In the games favor, it IS presented in the best possible way... annoying, but kind fun).
EDIT: Can't forget the lack of a second region. Yeah, a second region... that would have not only been butchered, but would have butchered the main reason.